Re: [AMBER] Error in Installing Amber 20 on GPU

From: Suchetana Gupta <tutulg.gmail.com>
Date: Tue, 30 Jun 2020 09:00:46 +0530

Hi Dave
Yes, we did modify -DCUDA=TRUE in the CMake script.
I am putting the log file as text here:
make[2]: Entering directory '/home/sks/Desktop/SUCHETANA/amber20/test'
cd cuda && make -k test.pmemd.cuda PREC_MODEL=DPFP
make[3]: Entering directory '/home/sks/Desktop/SUCHETANA/amber20/test/cuda'
------------------------------------
Running CUDA Implicit solvent tests.
  Precision Model = DPFP
------------------------------------
cd gb_ala3/ && ./Run.igb1_ntc1_min DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.igb1_ntc1_min: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb1_ntc1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb1_ntc1: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest0_ntt0_igb1_ntc1_hotstart DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest0_ntt0_igb1_ntc1_hotstart: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest0_ntt0_igb1_ntc1_coldstart DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest0_ntt0_igb1_ntc1_coldstart: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb1_ntc2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb1_ntc2: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb2_ntc1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb2_ntc1: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb2_ntc2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb2_ntc2: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb5_ntc1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb5_ntc1: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb7_ntc2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb7_ntc2: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb8_ntc2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb8_ntc2: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb5_ntc2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb5_ntc2: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb5_ntc2_ntr1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb5_ntc2_ntr1: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb5_ntc2_saltcon DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb5_ntc2_saltcon: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb5_ntc2_rgbmax DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb5_ntc2_rgbmax: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt0_igb5_ntc2_alpb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt0_igb5_ntc2_alpb: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt1_igb1_ntc2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt1_igb1_ntc2: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt2_igb1_ntc2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt2_igb1_ntc2: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd gb_ala3/ && ./Run.irest1_ntt3_igb1_ntc2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.irest1_ntt3_igb1_ntc2: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd nmropt/gb/multi-angle/ && ./Run.nmropt_2angle_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_2angle_gb: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd nmropt/gb/angle_torsion_com/ && ./Run.angdih_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.angdih_gb: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd chamber/dhfr/ && ./Run.dhfr_charmm.min DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_charmm.min: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd chamber/dhfr_cmap/ && ./Run.dhfr_charmm.min DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_charmm.min: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
cd nucleosome/ && ./Run_min.1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_min.1: Program error
Makefile:30: recipe for target 'test.pmemd.cuda.gb.serial' failed
make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored)
---------------------------------------------
Running Extended CUDA Implicit solvent tests.
      Precision Model = DPFP
---------------------------------------------
cd trpcage/ && ./Run_md_trpcage DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_md_trpcage: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd myoglobin/ && ./Run_md_myoglobin DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_md_myoglobin: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd myoglobin/ && ./Run_md_myoglobin_igb7 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_md_myoglobin_igb7: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd myoglobin/ && ./Run_md_myoglobin_igb8 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_md_myoglobin_igb8: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd myoglobin/ && ./Run_md_myoglobin_igb8_gbsa DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_md_myoglobin_igb8_gbsa: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd myoglobin/ && ./Run_md_myoglobin_igb8_gbsa3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_md_myoglobin_igb8_gbsa3: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd gbsa_xfin/ && ./Run.gbsa3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.gbsa3: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd cnstph/implicit/ && ./Run.cnstph DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.cnstph: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd cnste/implicit/ && ./Run.cnste DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.cnste: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd cnstphe/implicit/ && ./Run.cnstphe DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.cnstphe: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd chamber/dhfr/ && ./Run.dhfr_charmm.md DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_charmm.md: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd chamber/dhfr_cmap/ && ./Run.dhfr_charmm.md DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_charmm.md: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nucleosome/ && ./Run_md.1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_md.1: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nucleosome/ && ./Run_md.2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_md.2: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd amd/rna_gb && ./Run.gb.amd1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.gb.amd1: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd amd/rna_gb && ./Run.gb.amd2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.gb.amd2: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd amd/rna_gb && ./Run.gb.amd3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.gb.amd3: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/angle/ && ./Run.nmropt_1angle_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_1angle_gb: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/distance/ && ./Run.dist_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
errori: label not found.
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/distance_COM/ && ./Run.distCOM_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.distCOM_gb: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/distance_COM/ && ./Run.distr6av_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.distr6av_gb: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/jar_distance_COM/ && ./Run.jar_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.jar_gb: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/jar_distance/ && ./Run.jar_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.jar_gb: Program Error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/jar_torsion/ && ./Run.jar_torsion DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.jar_torsion: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/nmropt_1_torsion/ && ./Run.nmropt_1_torsion DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_1_torsion: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/tautp/ && ./Run.nmropt_1tautp_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_1tautp_gb: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/temp/ && ./Run.nmropt_1temp_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_1temp_gb: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
cd nmropt/gb/angle_torsion_com/ && ./Run.angdih_gb DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.angdih_gb: Program error
Makefile:60: recipe for target 'test.pmemd.cuda.gb' failed
make[3]: [test.pmemd.cuda.gb] Error 1 (ignored)
---------------------------------------------
Running Extended CUDA Explicit solvent tests.
      Precision Model = DPFP
---------------------------------------------
cd 4096wat/ && ./Run.pure_wat DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pure_wat: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd 4096wat/ && ./Run.pure_wat_fswitch DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pure_wat_fswitch: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd 4096wat/ && ./Run.pure_wat_efield DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pure_wat_efield: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd 4096wat_oct/ && ./Run.pure_wat_oct_NVE DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pure_wat_oct_NVE: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd 4096wat_oct/ && ./Run.pure_wat_oct_NVT_NTT1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pure_wat_oct_NVT_NTT1: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd 4096wat_oct/ && ./Run.pure_wat_oct_NPT_NTT1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pure_wat_oct_NPT_NTT1: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd large_solute_count/ && ./Run.ntb2_ntt1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.ntb2_ntt1: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd jac/ && ./Run.jac DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.jac: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr.ntr1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr.ntr1: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr.ntb2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr.ntb2: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr.ntb2_ntt1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr.ntb2_ntt1: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr.ntb2_ntt1_ntr1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr.ntb2_ntt1_ntr1: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr.noshake DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr.noshake: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd chamber/dhfr_pbc/ && ./Run.dhfr_pbc_charmm_noshake.md DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_pbc_charmm_noshake.md: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm.md DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_cmap_pbc_charmm.md: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm_NPT.md DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_cmap_pbc_charmm_NPT.md: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm_noshake.md DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_cmap_pbc_charmm_noshake.md: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd ips/ && ./Run.ips DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.ips: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd amd/dhfr_pme && ./Run.pme.amd1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pme.amd1: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd amd/dhfr_pme && ./Run.pme.amd2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pme.amd2: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd amd/dhfr_pme && ./Run.pme.amd3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pme.amd3: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd amd/gact_ips && ./Run.ips.amd1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.ips.amd1: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd amd/gact_ips && ./Run.ips.amd2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.ips.amd2: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd amd/gact_ips && ./Run.ips.amd3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.ips.amd3: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd scaledMD && ./Run.scaledMD DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.scaledMD: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/angle/ && ./Run.nmropt_1angle_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_1angle_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/distance/ && ./Run.dist_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dist_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/distance_COM/ && ./Run.distCOM_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.distCOM_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/distance_COM/ && ./Run.multi-distCOM-multi-dist_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.multi-distCOM-multi-dist_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/distance_COM/ && ./Run.multi-distr6av_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.multi-distr6av_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/jar_distance_COM/ && ./Run.jar_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.jar_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/jar_distance/ && ./Run.jar_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.jar_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/jar_torsion/ && ./Run.jar_torsion DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.jar_torsion: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/nmropt_1_torsion/ && ./Run.nmropt_1_torsion DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_1_torsion: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/angle_torsion_com/ && ./Run.angdihmultCOM DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.angdihmultCOM: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/tautp/ && ./Run.nmropt_1tautp_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_1tautp_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd nmropt/pme/temp/ && ./Run.nmropt_1temp_pbc DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.nmropt_1temp_pbc: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip4pew/ && ./Run.tip4pew_box_nvt DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip4pew_box_nvt: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip4pew/ && ./Run.tip4pew_box_npt DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip4pew_box_npt: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip4pew/ && ./Run.tip4pew_oct_nvt DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip4pew_oct_nvt: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip4pew/ && ./Run.tip4pew_oct_npt DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip4pew_oct_npt: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip4pew/ && ./Run.tip4pew_box_npt_mcbar DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip4pew_box_npt_mcbar: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip4pew/ && ./Run.tip4pew_oct_npt_mcbar DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip4pew_oct_npt_mcbar: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip5p/ && ./Run.tip5p_box_nvt DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip5p_box_nvt: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip5p/ && ./Run.tip5p_box_npt DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip5p_box_npt: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip5p/ && ./Run.tip5p_oct_nvt DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip5p_oct_nvt: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd tip5p/ && ./Run.tip5p_oct_npt DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.tip5p_oct_npt: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd HMR/ && ./Run.HMR DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.HMR: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd lipid_npt_tests/ && ./Run_npt_isotropic.lipid14 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_npt_isotropic.lipid14: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd lipid_npt_tests/ && ./Run_npt_anisotropic.lipid14 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_npt_anisotropic.lipid14: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
cd lipid_npt_tests/ && ./Run_npt_semiisotropic.lipid14 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run_npt_semiisotropic.lipid14: Program error
Makefile:140: recipe for target 'test.pmemd.cuda.pme' failed
make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
------------------------------------
Running CUDA Explicit solvent tests.
  Precision Model = DPFP
------------------------------------
cd 4096wat/ && ./Run.vrand DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.vrand: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd 4096wat_oct/ && ./Run.pure_wat_oct_NVT_NTT2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pure_wat_oct_NVT_NTT2: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd 4096wat_oct/ && ./Run.pure_wat_oct_NVT_NTT3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pure_wat_oct_NVT_NTT3: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr.ntb2_ntt3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr.ntb2_ntt3: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd ips/ && ./Run.ips_ntt3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.ips_ntt3: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd npt_ntr_ntt3_oct/ && ./Run.ntp1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.ntp1: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr.min DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr.min: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd mcwat && ./Run.mcwat DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.mcwat: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd RAMD && ./Run.ramd DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.ramd: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd chamber/dhfr_pbc/ && ./Run.dhfr_pbc_charmm_noshake.min DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_pbc_charmm_noshake.min: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm.min DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_cmap_pbc_charmm.min: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd chamber/dhfr_cmap_pbc/ && ./Run.dhfr_cmap_pbc_charmm_noshake.min DPFP
yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_cmap_pbc_charmm_noshake.min: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd cnstph/explicit/ && ./Run.cnstph DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.cnstph: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd cnste/explicit/ && ./Run.cnste DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.cnste: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd cnstphe/explicit/ && ./Run.cnstphe DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.cnstphe: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd nfe/ && ./run-pmemd-serial.sh DPFP yes
>>>>>>> doing 'abmd_ANALYSIS'
 ** Error ** : '/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP' is
not executable
>>>>>>> doing 'abmd_FLOODING'
 ** Error ** : '/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP' is
not executable
>>>>>>> doing 'abmd_UMBRELLA'
 ** Error ** : '/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP' is
not executable
>>>>>>> doing 'smd'
 ** Error ** : '/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP' is
not executable
>>>>>>> doing 'smd2'
 ** Error ** : '/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP' is
not executable
>>>>>>> doing 'pmd'
 ** Error ** : '/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP' is
not executable
cd ff19SB/ && ./Run DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd dhfr/ && ./Run.dhfr_reweight DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dhfr_reweight: Program error
Makefile:105: recipe for target 'test.pmemd.cuda.pme.serial' failed
make[3]: [test.pmemd.cuda.pme.serial] Error 1 (ignored)
cd gamd/rna_gb && ./Run.gb.gamd1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.gb.gamd1: Program error
Makefile:95: recipe for target 'test.pmemd.cuda.gb.gamd' failed
make[3]: [test.pmemd.cuda.gb.gamd] Error 1 (ignored)
cd gamd/rna_gb && ./Run.gb.gamd2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.gb.gamd2: Program error
Makefile:95: recipe for target 'test.pmemd.cuda.gb.gamd' failed
make[3]: [test.pmemd.cuda.gb.gamd] Error 1 (ignored)
cd gamd/rna_gb && ./Run.gb.gamd3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.gb.gamd3: Program error
Makefile:95: recipe for target 'test.pmemd.cuda.gb.gamd' failed
make[3]: [test.pmemd.cuda.gb.gamd] Error 1 (ignored)
cd gamd/dhfr_pme && ./Run.pme.gamd1 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pme.gamd1: Program error
Makefile:199: recipe for target 'test.pmemd.cuda.pme.gamd' failed
make[3]: [test.pmemd.cuda.pme.gamd] Error 1 (ignored)
cd gamd/dhfr_pme && ./Run.pme.gamd2 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pme.gamd2: Program error
Makefile:199: recipe for target 'test.pmemd.cuda.pme.gamd' failed
make[3]: [test.pmemd.cuda.pme.gamd] Error 1 (ignored)
cd gamd/dhfr_pme && ./Run.pme.gamd3 DPFP yes
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.pme.gamd3: Program error
Makefile:199: recipe for target 'test.pmemd.cuda.pme.gamd' failed
make[3]: [test.pmemd.cuda.pme.gamd] Error 1 (ignored)
------------------------------------
Running CUDA GTI free energy tests.
cd gti/Na/ && ./Run.NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/Na
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVE: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/Na/ && ./Run.NVT_ntt1 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/Na
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt1: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/Na/ && ./Run.NVT_ntt3 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/Na
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt3: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/Na/ && ./Run.NPT_BR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/Na
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NPT_BR: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/Na/ && ./Run.NPT_MC DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/Na
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NPT_MC: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/Na/ && ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/Na
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/Na/ && ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/Na
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/Na/ && ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/Na
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/ligand/ && ./Run.NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVE: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/ligand/ && ./Run.NVT_ntt1 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt1: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/ligand/ && ./Run.NVT_ntt3 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt3: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/ligand/ && ./Run.NPT_BR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NPT_BR: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/ligand/ && ./Run.NPT_MC DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NPT_MC: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/ligand/ && ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/ligand/ && ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/ligand/ && ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/complex/ && ./Run.NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVE: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/complex/ && ./Run.NVT_ntt1 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt1: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/complex/ && ./Run.NVT_ntt3 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt3: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/complex/ && ./Run.NPT_BR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NPT_BR: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/complex/ && ./Run.NPT_MC DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NPT_MC: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/complex/ && ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/complex/ && ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/AFE_TI/campTI && ./Run.campTI DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/AFE_TI/campTI
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.campTI: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/AFE_TI/softcore/complex && ./Run.complex DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/AFE_TI/softcore/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.complex: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/AFE_TI/softcore/electro && ./Run.electro DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/AFE_TI/softcore/electro
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.electro: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/AFE_TI/softcore/dynlmb && ./Run.dynlmb DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/AFE_TI/softcore/dynlmb
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.dynlmb: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/AFE_MBAR/campMBAR && ./Run.campMBAR DPFP SCH=222 ./Run.SC_NVT_MBAR
SPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/AFE_MBAR/campMBAR
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.campMBAR: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/AFE_MBAR/softcore/complex && ./Run.complex DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/AFE_MBAR/softcore/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.complex: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
cd gti/AFE_MBAR/softcore/electro && ./Run.electro DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/AFE_MBAR/softcore/electro
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.electro: Program error
Makefile:240: recipe for target 'test.pmemd.cuda.gti.TI' failed
make[3]: [test.pmemd.cuda.gti.TI] Error 1 (ignored)
------------------------------------
Running CUDA GTI NMR Restratin tests.
cd gti/NMR_Restraint/SimpleTorsion && CASE=A ./Run DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/NMR_Restraint/SimpleTorsion
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run: Program error
Makefile:275: recipe for target 'test.pmemd.cuda.gti.TI_restraint' failed
make[3]: [test.pmemd.cuda.gti.TI_restraint] Error 1 (ignored)
cd gti/NMR_Restraint/SimpleTorsion && CASE=B ./Run DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/NMR_Restraint/SimpleTorsion
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run: Program error
Makefile:275: recipe for target 'test.pmemd.cuda.gti.TI_restraint' failed
make[3]: [test.pmemd.cuda.gti.TI_restraint] Error 1 (ignored)
cd gti/NMR_Restraint/SimpleTorsion && CASE=C ./Run DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/NMR_Restraint/SimpleTorsion
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run: Program error
Makefile:275: recipe for target 'test.pmemd.cuda.gti.TI_restraint' failed
make[3]: [test.pmemd.cuda.gti.TI_restraint] Error 1 (ignored)
#Begin GTI Tests
------------------------------------
Running CUDA GTI 12-6-4 tests.
cd gti/1264/MgMD && ./Run.NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/1264/MgMD
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT: Program error
Makefile:282: recipe for target 'test.pmemd.cuda.gti.1264' failed
make[3]: [test.pmemd.cuda.gti.1264] Error 1 (ignored)
cd gti/1264/2ionMD && ./Run.NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/1264/2ionMD
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT: Program error
Makefile:282: recipe for target 'test.pmemd.cuda.gti.1264' failed
make[3]: [test.pmemd.cuda.gti.1264] Error 1 (ignored)
cd gti/1264/Mg2Zn && ./Run.NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/1264/Mg2Zn
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT: Program error
Makefile:282: recipe for target 'test.pmemd.cuda.gti.1264' failed
make[3]: [test.pmemd.cuda.gti.1264] Error 1 (ignored)
cd gti/1264/SimpleTI && ./Run DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/1264/SimpleTI
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run: Program error
Makefile:282: recipe for target 'test.pmemd.cuda.gti.1264' failed
make[3]: [test.pmemd.cuda.gti.1264] Error 1 (ignored)
#Begin GTI Tests
------------------------------------
Running CUDA GTI BAT tests.
cd gti/BAT/Simple && DIR=for ./Run DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/BAT/Simple
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run: Program error
Makefile:291: recipe for target 'test.pmemd.cuda.gti.BAT' failed
make[3]: [test.pmemd.cuda.gti.BAT] Error 1 (ignored)
cd gti/BAT/Simple && DIR=back ./Run DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/BAT/Simple
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run: Program error
Makefile:291: recipe for target 'test.pmemd.cuda.gti.BAT' failed
make[3]: [test.pmemd.cuda.gti.BAT] Error 1 (ignored)
#Begin GTI Tests
------------------------------------
Running CUDA GTI Lambda Scheduling.
cd gti/LambdaScheduling/complex/ && SCH=222 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/LambdaScheduling/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:331: recipe for target 'test.pmemd.cuda.gti.LambdaScheduling'
failed
make[3]: [test.pmemd.cuda.gti.LambdaScheduling] Error 1 (ignored)
cd gti/LambdaScheduling/complex/ && SCH=333 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/LambdaScheduling/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:331: recipe for target 'test.pmemd.cuda.gti.LambdaScheduling'
failed
make[3]: [test.pmemd.cuda.gti.LambdaScheduling] Error 1 (ignored)
cd gti/LambdaScheduling/complex/ && SCH=444 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/LambdaScheduling/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:331: recipe for target 'test.pmemd.cuda.gti.LambdaScheduling'
failed
make[3]: [test.pmemd.cuda.gti.LambdaScheduling] Error 1 (ignored)
cd gti/LambdaScheduling/complex/ && SCH=22T ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/LambdaScheduling/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:331: recipe for target 'test.pmemd.cuda.gti.LambdaScheduling'
failed
make[3]: [test.pmemd.cuda.gti.LambdaScheduling] Error 1 (ignored)
#Begin GTI Tests
------------------------------------
Running CUDA GTI free energy SC correction tests.
cd gti/SC_Correction/methane_2_methanol/ && SC_CORR=0 ./Run.NVT_ntt3 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/methane_2_methanol
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt3: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/methane_2_methanol/ && SC_CORR=-1 ./Run.NVT_ntt3 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/methane_2_methanol
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt3: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/methane_2_methanol/ && SC_CORR=1 ./Run.NVT_ntt3 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/methane_2_methanol
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt3: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/methane_2_methanol/ && SC_CORR=2 ./Run.NVT_ntt3 DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/methane_2_methanol
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.NVT_ntt3: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=0 ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=-1 ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=1 ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=2 ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=0 ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=-1 ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=1 ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=2 ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=0 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=-1 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=1 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/ligand/ && SC_CORR=2 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/ligand
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=0 ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=-1 ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=1 ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=2 ./Run.SC_NVE DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVE: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=0 ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=-1 ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=1 ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=2 ./Run.SC_NVT DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=0 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=-1 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=1 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
cd gti/SC_Correction/complex/ && SC_CORR=2 ./Run.SC_NVT_MBAR DPFP
/home/sks/Desktop/SUCHETANA/amber20/test/cuda/gti/SC_Correction/complex
/home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
  ./Run.SC_NVT_MBAR: Program error
Makefile:298: recipe for target 'test.pmemd.cuda.gti.SC_Correction' failed
make[3]: [test.pmemd.cuda.gti.SC_Correction] Error 1 (ignored)
make[3]: Leaving directory '/home/sks/Desktop/SUCHETANA/amber20/test/cuda'
make[2]: Leaving directory '/home/sks/Desktop/SUCHETANA/amber20/test'
make[2]: Entering directory '/home/sks/Desktop/SUCHETANA/amber20/test'

Finished CUDA test suite for Amber 20 at Mon Jun 29 16:00:01 IST 2020.

make[2]: Leaving directory '/home/sks/Desktop/SUCHETANA/amber20/test'
0 file comparisons passed
0 file comparisons failed
196 tests experienced errors


And outputs from the previous steps are:

Followed instructions mentioned in Amber20 Manual, Section 20.6.5

Output of ./run_cmake :



-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.9.0
-- For how to use this build system, please read this wiki:
-- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
-- For a list of important CMake variables, check here:
-- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options

-- 
**************************************************************************
-- Amber source found, building AmberTools and Amber
-- Miniconda is installed in the build directory!
-- Found perl make: /usr/bin/make
-- Perl modules well be installed to AMBERHOME/lib/perl
-- Running updater...
-- >>> Preparing to apply updates... please wait.
-- >>> No new updates available for AmberTools 20
-- >>> No new updates available for Amber 20
-- Updater done.  If you want to install updates, then set the
APPLY_UPDATES variable to true.
-- Checking whether to use built-in libraries...
-- Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY
READLINE_IS_LINKABLE)
-- Could NOT find Termcap (missing: TERMCAP_LIBRARY TERMCAP_INCLUDE_DIR)
-- Cannot use internal readline because its dependency
(libtermcap/libtinfo/libncurses) was not found.
-- Unable to locate MKL_HOME for your system.  To use MKL, set MKL_HOME to
point to your MKL installation location.
-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY
MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY)
-- Cannot search for FFTW Fortran headers because the serial headers were
not found
-- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS
FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS)
-- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 =
NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 =
NetCDF_LIBRARIES_F77-NOTFOUND)
-- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 =
NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 =
NetCDF_LIBRARIES_F90-NOTFOUND)
-- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES
NetCDF_INCLUDES)
-- Could NOT find xblas.  Please set XBLAS_LIBRARY to point to libxblas.a.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- The ARPACK library was not found.  Please set ARPACK_LIBRARY to point to
it. (missing: ARPACK_LIBRARY ARPACK_WORKS)
-- Could not find some or all of the five main APBS libraries. Please set
APBS_GENERIC_LIB, APBS_ROUTINES_LIB,
APBS_PMGC_LIB, APBS_MG_LIB, and APBS_MALOC_LIB to point to the correct
libraries (missing: APBS_API_LIB APBS_ROUTINES_LIB APBS_MG_LIB
APBS_PMGC_LIB APBS_GENERIC_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES)
-- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2
JAVA_AWT_INCLUDE_PATH)
-- Could not find the Java development libraries, so PUPIL can't be used.
(missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB)
-- Could not find lio.  If you want to use it, set LIO_HOME to point to a
built lio source directory.
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769
(message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873
(_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501
(_Boost_MISSING_DEPENDENCIES)
  cmake/3rdPartyTools.cmake:526 (find_package)
  CMakeLists.txt:194 (include)
-- Boost version: 1.65.1
-- Found the following Boost libraries:
--   thread
--   system
--   program_options
--   iostreams
--   regex
--   timer
--   chrono
--   filesystem
--   graph
-- Could NOT find MBX (missing: MBX_DIR)
-- Could not find MBX.  To locate it, add its install dir to the prefix
path.
-- The following libraries were found on your system, but are not being
used: boost
-- This is because the Amber devs have frequently seen broken installs of
these libraries causing trouble.
-- To tell Amber to link to these libraries, you can select individual ones
using -DFORCE_EXTERNAL_LIBS=<names>.
-- Alternatively, you can request that Amber link to all libraries it finds
using -DTRUST_SYSTEM_LIBS=TRUE.
-- Cannot find PLUMED.  You will still be able to load it at runtime.  If
you want to link it at build time, set PLUMED_ROOT to where you installed
it.
-- Generating amber source scripts
-- Configuring subdirs...
-- FFTW: compiler supports stack alignment: TRUE
-- Found bash: /bin/bash
-- netcdf-fortran: Detected TS29113 support in Fortran compiler
-- Reticulating splines...
If you can't see the following build report, then you need to turn off
COLOR_CMAKE_MESSAGES
-- 
**************************************************************************
--                               Build Report
--                              Compiler Flags:
-- C No-Opt:           -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable -O0
-- C Optimized:        -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native
--
-- CXX No-Opt:         -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-local-typedefs -Wno-unused-variable
-Wno-unused-but-set-variable -O0
-- CXX Optimized:      -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-local-typedefs -Wno-unused-variable
-Wno-unused-but-set-variable -O3 -mtune=native
--
-- Fortran No-Opt:     -Wall -Wno-tabs -Wno-unused-function
-ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O0
-- Fortran Optimized:  -Wall -Wno-tabs -Wno-unused-function
-ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O3
-mtune=native
--
--                           3rd Party Libraries
-- ---building bundled:
-----------------------------------------------------
-- arpack - for fundamental linear algebra calculations
-- ucpp - used as a preprocessor for the NAB compiler
-- netcdf - for creating trajectory data files
-- netcdf-fortran - for creating trajectory data files from Fortran
-- fftw - used to do Fourier transforms very quickly
-- xblas - used for high-precision linear algebra calculations
-- boost - C++ support library
-- ---using installed:
------------------------------------------------------
-- blas - for fundamental linear algebra calculations
-- lapack - for fundamental linear algebra calculations
-- zlib - for various compression and decompression tasks
-- libbz2 - for bzip2 compression in cpptraj
-- libm - for fundamental math routines if they are not contained in the C
library
-- perlmol - chemistry library used by FEW
-- ---disabled: ------------------------------------------------
-- c9x-complex - used as a support library on systems that do not have C99
complex.h support
-- readline - used for the console functionality of cpptraj
-- lio - used by Sander to run certain QM routines on the GPU
-- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver
-- pupil - used by Sander as an alternate user interface
-- plumed - used as an alternate MD backend for Sander
-- mkl - alternate implementation of lapack and blas that is tuned for speed
-- mbx - computes energies and forces for pmemd with the MB-pol model
--                                Features:
-- MPI:                     OFF
-- OpenMP:                  OFF
-- CUDA:                    OFF
-- Build Shared Libraries:  ON
-- Build GUI Interfaces:    ON
-- Build Python Programs:   ON
--  -Python Interpreter:    Internal Miniconda (version 3.7)
-- Build Perl Programs:     ON
-- Build configuration:     RELEASE
-- Target Processor:        x86_64
-- Build Documentation:     OFF
-- Sander Variants:         normal LES API LES-API
-- Install location:        /home/sks/Desktop/SUCHETANA/amber20/
-- Installation of Tests:   ON
--                               Compilers:
--         C: GNU 7.5.0 (/usr/bin/gcc)
--       CXX: GNU 7.5.0 (/usr/bin/g++)
--   Fortran: GNU 7.5.0 (/usr/bin/gfortran)
--                              Building Tools:
-- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc
few gbnsr6 gem.pmemd leap lib mdgx mm_pbsa mmpbsa_py moft nab ndiff-2.00
nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa
pdb4amber pmemd pymsmt pysander pytraj reduce rism sander saxs sebomd sff
sqm xray xtalutil
--                            NOT Building Tools:
-- quick - In-development programs are disabled.
-- pymdgx - In-development programs are disabled.
-- gpu_utils - Requires CUDA
-- 
**************************************************************************
-- Environment resource files are provided to set the proper environment
-- variables to use AMBER and AmberTools. This is required to run any Python
-- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
--
-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
-- /home/sks/Desktop/SUCHETANA/amber20//amber.sh file in your shell.
Consider adding the line
--   test -f /home/sks/Desktop/SUCHETANA/amber20//amber.sh && source
/home/sks/Desktop/SUCHETANA/amber20//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /home/sks/Desktop/SUCHETANA/amber20//amber.csh file in your shell.
Consider adding the line
--   test -f /home/sks/Desktop/SUCHETANA/amber20//amber.csh && source
/home/sks/Desktop/SUCHETANA/amber20//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- Amber will be installed to /home/sks/Desktop/SUCHETANA/amber20/
-- Configuring done
-- Generating done
-- Build files have been written to:
/home/sks/Desktop/SUCHETANA/amber20_src/build
If the cmake build report looks OK, you should now do the following:
    make install
    source /home/sks/Desktop/SUCHETANA/amber20/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
Output of make install:
[  1%] Built target ucpp
[  2%] Built target fftw3_threads_obj
[  3%] Built target fftw_api
[  3%] Built target dft
[  4%] Built target dft_scalar
[  5%] Built target dft_scalar_codelets
[ 10%] Built target dft_sse2_codelets
[ 11%] Built target rdft
[ 11%] Built target rdft_scalar
[ 14%] Built target rdft_scalar_r2cb
[ 16%] Built target rdft_scalar_r2cf
[ 16%] Built target rdft_scalar_r2r
[ 17%] Built target rdft_sse2_codelets
[ 18%] Built target fftw_kernel
[ 18%] Built target reodft
[ 18%] Built target simd_support
[ 18%] Built target fftw
[ 19%] Built target libfftw_bench
[ 20%] Built target fftw_benchmark_common_obj
[ 20%] Built target fftw_benchmark
[ 20%] Built target fftw_wisdom
[ 21%] Built target dispatch
[ 21%] Built target netcdf3
[ 22%] Built target netcdf
[ 23%] Built target ncgen
[ 23%] Built target ncgen3
[ 23%] Built target nccopy
[ 23%] Built target ncdump
[ 24%] Built target netcdff
[ 24%] Built target xblas_build
[ 25%] Built target arpack
[ 25%] Built target boost_build
[ 25%] Built target amber_common
[ 27%] Built target rism
[ 28%] Built target libpbsa
[ 28%] Built target dsarpack_obj
[ 28%] Built target sff_lex
[ 28%] Built target sff_rism_interface
[ 28%] Built target sff
[ 29%] Built target gbnsr6
[ 29%] Built target cifparse
[ 30%] Built target addles
[ 31%] Built target ambmask
[ 31%] Built target sander_rism_interface
[ 33%] Built target sqm_common
[ 33%] Built target libsqm
[ 33%] Built target sff_fortran
[ 38%] Built target sander_base_obj
[ 41%] Built target sebomd
[ 41%] Built target emil
[ 42%] Built target pbsa_sander
[ 48%] Built target libsander
[ 48%] Built target sander
[ 54%] Built target sander.LES
[ 59%] Built target libsanderles
[ 59%] Built target makeANG_RST
[ 59%] Built target makeDIST_RST
[ 59%] Built target nef_to_RST
[ 61%] Built target nmode
[ 61%] Built target antechamber_eprintf_obj
[ 61%] Built target parmcal
[ 61%] Built target espgen
[ 61%] Built target antechamber
[ 61%] Built target am1bcc
[ 61%] Built target test-penalties
[ 61%] Built target test-combination
[ 61%] Built target prepgen
[ 61%] Built target bondtype.orig
[ 61%] Built target parmchk2
[ 61%] Built target residuegen
[ 61%] Built target atomtype
[ 61%] Built target respgen
[ 61%] Built target bondtype
[ 61%] Built target test-int-part
[ 61%] Built target sqm
[ 61%] Built target pdb++
[ 62%] Built target reduce-tools
[ 62%] Built target reduce
[ 62%] Built target ndiff
[ 65%] Built target gem.pmemd
[ 65%] Built target add_xray
[ 65%] Built target add_pdb
[ 65%] Built target cpptraj_parm
[ 65%] Built target xdrfile
[ 75%] Built target cpptraj_common_obj
[ 75%] Built target libcpptraj
[ 76%] Built target cpptraj_core
[ 76%] Built target cpptraj
[ 77%] Built target cpptraj_traj
[ 78%] Built target cpptraj_file
[ 78%] Built target ambpdb
[ 80%] Built target pbsa
[ 81%] Built target simplepbsa
[ 81%] Built target hcp_getpdb
[ 81%] Built target rism3d.orave
[ 81%] Built target rism3d.snglpnt
[ 81%] Built target rism1d
[ 81%] Built target rism3d.thermo
[ 81%] Built target nab
[ 81%] Built target rule_parse
[ 81%] Built target nab_checkexpr_obj
[ 81%] Built target nab_lex
[ 82%] Built target nab2c
[ 82%] Built target mpinab2c
[ 84%] Built target libnab
[ 84%] Built target molsurf
[ 84%] Built target elsize
[ 84%] Built target resp
[ 84%] Built target gwh
[ 84%] Built target tinker_to_amber
[ 85%] Built target mdgx_common_obj
[ 85%] Built target mdgx
[ 85%] Built target libmdgx
[ 85%] Built target Xtal
[ 85%] Built target AddToBox
[ 85%] Built target UnitCell
[ 85%] Built target ChBox
[ 85%] Built target PropPDB
[ 85%] Built target saxs_common_obj
[ 85%] Built target saxs_rism
[ 85%] Built target saxs_md
[ 86%] Built target libsaxs_md
[ 86%] Built target libsaxs_rism
[ 86%] Built target mm_pbsa_nabnmode
[ 86%] Built target make_crd_hg
[ 87%] Built target paramfit
[ 87%] Built target draw_membrane2
[ 87%] Built target minab
[ 87%] Built target ffgbsa
[ 87%] Built target mdnab
[ 87%] Built target cestats
[ 88%] Built target cphstats
[ 88%] Built target nfe-umbrella-slice
[ 88%] Built target wcleap
[ 89%] Built target Xmu
[ 90%] Built target Xpm
[ 91%] Built target Xaw
[ 92%] Built target leap_general_obj
[ 92%] Built target utilMakeHelp
[ 93%] Built target leap_leap_obj
[ 93%] Built target leap_terminal_obj
[ 93%] Built target leap_hierarchy_obj
[ 94%] Built target xleap_resources
[ 94%] Built target leap_xleap_obj
[ 94%] Built target leap_common_obj
[ 94%] Built target leap_athena_obj
[ 94%] Built target teLeap
[ 94%] Built target xaLeap
[ 94%] Built target parmed
[ 94%] Built target mmpbsa_py_energy
[ 94%] Built target mmpbsa_py_nabnmode
[ 94%] Built target pysander
[ 94%] Building pytraj native library
sys.argv ['setup.py', 'build', '-b',
'/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build',
'--disable-openmp']
Original compiler envs
CXX = /usr/bin/g++
CC = /usr/bin/gcc
COMPILER =
use_pip = False, cpptraj_home =
compile_c_extension = True
2.0.5
use_prebuilt_cythonized_files =  False
pytraj is inside AMBERHOME
using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++
using CC=/usr/bin/gcc, CXX=/usr/bin/g++
Final compiler envs
CXX = /usr/bin/g++
CC = /usr/bin/gcc
COMPILER =
install = True
set rpath to
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/cpptraj/src
running build
running build_py
copying pytraj/version.py ->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-3.7/pytraj
running build_ext
[ 94%] Built target pytraj
[ 95%] Built target memembed
[ 96%] Built target packmol
[ 96%] Built target metatwist
[100%] Built target pmemd
Install the project...
-- Install configuration: "RELEASE"
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/./amber.sh
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/./amber.csh
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/lib/python3.7/site-packages/conda_build/convert.py
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/f2py
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/cython
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/c_rehash
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/wheel
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/chardetect
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/pytest
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-nbconvert
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/pyvenv-3.7
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/f2py3.7
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-serverextension
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-build
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/zstdgrep
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/sqlite3_analyzer
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/idle3.7
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/pydoc3.7
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-kernelspec
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-metapackage
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/bzdiff
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/zstdless
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-kernel
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-run
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-convert
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/pkginfo
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/ipython
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-inspect
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/activate
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/iptest
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/bzmore
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/python3.7m-config
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/cph
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/ipython3
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-bundlerextension
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/pip3
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/cythonize
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/2to3-3.7
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jsonschema
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/pygmentize
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/cygdb
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/xzgrep
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/f2py3
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-render
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/py.test
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/xml2-config
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-skeleton
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-debug
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-index
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/iptest3
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/xzless
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-nbextension
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-trust
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/ncursesw6-config
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/tqdm
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/xzdiff
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-troubleshoot
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-develop
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-migrate
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/pip
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/xzmore
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/deactivate
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/icu-config
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/conda-env
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/bzgrep
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/easy_install
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/miniconda/bin/jupyter-notebook
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/fftw-wisdom-to-conf
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/nc-config
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/lib/libnetcdf.settings
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/lib/cmake/netCDF/netCDFTargets-release.cmake
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/nf-config
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/senergy
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/sviol
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/sviol2
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/am1bcc
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/atomtype
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/espgen
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/parmcal
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/parmchk2
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/prepgen
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/residuegen
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/respgen
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/antechamber
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/bondtype
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/bondtype.orig
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/reduce
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/XrayPrep
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/nab
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/sgldinfo.sh
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/sgldwt.sh
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/process_mdout.perl
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/process_minout.perl
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/mdout2pymbar.pl
running build
running build_py
running build_scripts
running install
running install_lib
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/windows.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/mdout.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/menus.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/constants.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/widgets.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/dataset.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/graphproperties.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/lib/mdoutanalyzer/toplevel_app.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/windows.py
to windows.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/mdout.py
to mdout.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/menus.py
to menus.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/constants.py
to constants.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/widgets.py
to widgets.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/dataset.py
to dataset.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/graphproperties.py
to graphproperties.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/mdoutanalyzer/toplevel_app.py
to toplevel_app.cpython-37.pyc
running install_scripts
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/scripts-3.7/ceinutil.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/scripts-3.7/softcore_setup.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/scripts-3.7/cpeinutil.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/scripts-3.7/fitpkaeo.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
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-> /home/sks/Desktop/SUCHETANA/amber20/bin
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-> /home/sks/Desktop/SUCHETANA/amber20/bin
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/scripts-3.7/cpinutil.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
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-> /home/sks/Desktop/SUCHETANA/amber20/bin
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/scripts-3.7/finddgref.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/etc/CMakeFiles/python-build/scripts-3.7/charmmlipid2amber.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/ceinutil.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/softcore_setup.py
to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/cpeinutil.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/fitpkaeo.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/fixremdcouts.py to
755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/genremdinputs.py
to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/cpinutil.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/mdout_analyzer.py
to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/finddgref.py to 755
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running install_egg_info
Removing
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Writing
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-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/mm_pbsa.pl
-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/mm_pbsa_statistics.pl
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running build
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-- Installing: /home/sks/Desktop/SUCHETANA/amber20/bin/tleap
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running build
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UPDATING
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set
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to 'at20RC5+54.g5702a232fe.dirty'
running build_ext
building 'parmed.amber._rdparm' extension
gcc -pthread -B
/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat
-Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC
-I/home/sks/Desktop/SUCHETANA/amber20_src/AmberTools/src/parmed/src
-I/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/include/python3.7m
-c src/_rdparm.cpp -o
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/parmed/CMakeFiles/parmed-build/temp.linux-x86_64-3.7/src/_rdparm.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
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gcc -pthread -B
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-Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC
-I/home/sks/Desktop/SUCHETANA/amber20_src/AmberTools/src/parmed/src
-I/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/include/python3.7m
-c src/readparm.cpp -o
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/parmed/CMakeFiles/parmed-build/temp.linux-x86_64-3.7/src/readparm.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
C/ObjC but not for C++
g++ -pthread -shared -B
/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat
-L/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/lib
-Wl,-rpath=/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/lib
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/parmed/CMakeFiles/parmed-build/temp.linux-x86_64-3.7/src/readparm.o
-o
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/parmed/CMakeFiles/parmed-build/lib.linux-x86_64-3.7/parmed/amber/_
rdparm.cpython-37m-x86_64-linux-gnu.so
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running install
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/formats/__init__.py
to __init__.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/formats/pqr.py
to pqr.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/formats/psf.py
to psf.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/formats/sdf.py
to sdf.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/formats/pdbx/__init__.py
to __init__.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/formats/pdbx/PdbxReader.py
to PdbxReader.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/formats/pdbx/PdbxContainers.py
to PdbxContainers.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/formats/pdbx/PdbxWriter.py
to PdbxWriter.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/titratable_residues.py
to titratable_residues.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/__init__.py
to __init__.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/amberformat.py
to amberformat.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/parameters.py
to parameters.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/netcdffiles.py
to netcdffiles.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/_amberparm.py
to _amberparm.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/_tinkerparm.py
to _tinkerparm.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/mdin/__init__.py
to __init__.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/mdin/cntrl.py
to cntrl.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/mdin/qmmm.py
to qmmm.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/mdin/ewald.py
to ewald.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/mdin/mdin.py
to mdin.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/mdin/pb.py
to pb.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/offlib.py
to offlib.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/readparm.py
to readparm.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/mask.py
to mask.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/asciicrd.py
to asciicrd.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/amber/_chamberparm.py
to _chamberparm.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/decorators.py
to decorators.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/__init__.py
to __init__.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/pairlist.py
to pairlist.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/timer.py
to timer.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/pandautils.py
to pandautils.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/netcdf.py
to netcdf.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/six.py
to six.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/_input.py
to _input.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/__init__.py
to __init__.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/_parser.py
to _parser.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/config.py
to config.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/_edit_descriptors.py
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/_lexer.py
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/_output.py
to _output.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/FortranRecordWriter.py
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/parmed/utils/fortranformat/_misc.py
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to residue.cpython-37.pyc
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to __init__.cpython-37.pyc
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to parameters.cpython-37.pyc
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running install_scripts
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/parmed/CMakeFiles/parmed-build/scripts-3.7/parmed
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
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-> /home/sks/Desktop/SUCHETANA/amber20/bin
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/parmed to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/xparmed to 755
running install_egg_info
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/ParmEd-at20RC5_54.g5702a232fe.dirty-py3.7.egg-info
Writing
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/ParmEd-at20RC5_54.g5702a232fe.dirty-py3.7.egg-info
/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.7/distutils/dist.py:274:
UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
running build
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/make_trajs.py
to make_trajs.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/parm_setup.py
to parm_setup.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/alamdcrd.py
to alamdcrd.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/findprogs.py
to findprogs.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/timer.py
to timer.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/API.py
to API.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/infofile.py
to infofile.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/output_file.py
to output_file.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/amber_outputs.py
to amber_outputs.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/fake_mpi.py
to fake_mpi.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/calculation.py
to calculation.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/exceptions.py
to exceptions.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/utils.py
to utils.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/commandlineparser.py
to commandlineparser.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/createinput.py
to createinput.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/input_parser.py
to input_parser.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA_mods/main.py
to main.cpython-37.pyc
running install_scripts
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/mmpbsa_py/CMakeFiles/python-build/scripts-3.7/ante-MMPBSA.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/mmpbsa_py/CMakeFiles/python-build/scripts-3.7/MMPBSA.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/ante-MMPBSA.py to
755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/MMPBSA.py to 755
running install_egg_info
Removing
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA.py-16.0-py3.7.egg-info
Writing
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/MMPBSA.py-16.0-py3.7.egg-info
running build
running build_py
running build_scripts
running install
running install_lib
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/ipmach/tifiles.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/ipmach
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/ipmach/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/ipmach
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/ipmach/calhfe.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/ipmach
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/ipmach/caliod.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/ipmach
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/lib.py
-> /home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/__init__.py
-> /home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/exp.py
-> /home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/sqmio.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/itfc_dict_table.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/getlist.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/cario.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/gmsio.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/pdbio.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/constants.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/element.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/amb2chm_typ.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/rstio.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/mol2io.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/cal.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/gauio.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mol/mol.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mcpb/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mcpb/gene_pre_frcmod_file.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mcpb/rename_residues.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mcpb/gene_final_frcmod_file.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mcpb/gene_model_files.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mcpb/amber_modeling.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/mcpb/resp_fitting.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/api/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/api
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/api/AmberParm.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/api
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/lib/pymsmt/title.py
-> /home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/ipmach/tifiles.py
to tifiles.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/ipmach/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/ipmach/calhfe.py
to calhfe.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/ipmach/caliod.py
to caliod.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/lib.py
to lib.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/exp.py
to exp.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/sqmio.py
to sqmio.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/itfc_dict_table.py
to itfc_dict_table.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/getlist.py
to getlist.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/cario.py
to cario.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/gmsio.py
to gmsio.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/pdbio.py
to pdbio.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/constants.py
to constants.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/element.py
to element.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/amb2chm_typ.py
to amb2chm_typ.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/rstio.py
to rstio.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/mol2io.py
to mol2io.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/cal.py
to cal.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/gauio.py
to gauio.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mol/mol.py
to mol.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py
to gene_pre_frcmod_file.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb/rename_residues.py
to rename_residues.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py
to gene_final_frcmod_file.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py
to gene_model_files.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb/amber_modeling.py
to amber_modeling.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/mcpb/resp_fitting.py
to resp_fitting.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/api/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/api/AmberParm.py
to AmberParm.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pymsmt/title.py
to title.cpython-37.pyc
running install_scripts
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/mol2rtf.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/amb2chm_psf_crd.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/metalpdb2mol2.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/car_to_files.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/espgen.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/ProScrs.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/MCPB.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/IPMach.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/CartHess2FC.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/amb2chm_par.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/PdbSearcher.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/OptC4.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pymsmt/CMakeFiles/python-build/scripts-3.7/amb2gro_top_gro.py
-> /home/sks/Desktop/SUCHETANA/amber20/bin
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/mol2rtf.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/amb2chm_psf_crd.py
to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/metalpdb2mol2.py
to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/car_to_files.py to
755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/espgen.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/ProScrs.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/MCPB.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/IPMach.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/CartHess2FC.py to
755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/amb2chm_par.py to
755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/PdbSearcher.py to
755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/OptC4.py to 755
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/amb2gro_top_gro.py
to 755
running install_egg_info
Removing
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pyMSMT-20.0-py3.7.egg-info
Writing
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/pyMSMT-20.0-py3.7.egg-info
running build
running build_py
running build_ext
running install
running install_lib
copying
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-> /home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/sander
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-3.7/sander/
pysander.cpython-37m-x86_64-linux-gnu.so ->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/sander
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-3.7/sanderles/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/sanderles
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-3.7/sanderles/
pysander.cpython-37m-x86_64-linux-gnu.so ->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/sanderles
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/sander/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/sanderles/__init__.py
to __init__.cpython-37.pyc
running install_egg_info
Removing
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/sander-16.0-py3.7.egg-info
Writing
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/sander-16.0-py3.7.egg-info
sys.argv ['./setup.py', 'build', '-b',
'/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build',
'--disable-openmp', 'install',
'--prefix=/home/sks/Desktop/SUCHETANA/amber20/']
Original compiler envs
CXX = /usr/bin/g++
CC = /usr/bin/gcc
COMPILER =
use_pip = False, cpptraj_home =
compile_c_extension = True
2.0.5
use_prebuilt_cythonized_files =  False
pytraj is inside AMBERHOME
using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++
using CC=/usr/bin/gcc, CXX=/usr/bin/g++
Final compiler envs
CXX = /usr/bin/g++
CC = /usr/bin/gcc
COMPILER =
install = True
set rpath to
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/cpptraj/src
running build
running build_py
copying pytraj/version.py ->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-3.7/pytraj
running build_ext
running install
running bdist_egg
running egg_info
writing pytraj.egg-info/PKG-INFO
writing dependency_links to pytraj.egg-info/dependency_links.txt
writing top-level names to pytraj.egg-info/top_level.txt
reading manifest file 'pytraj.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pytraj.egg-info/SOURCES.txt'
installing library code to
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg
running install_lib
creating
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg
creating
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj
creating
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/testing
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-3.7/pytraj/testing/testing.py
->
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copying
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->
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copying
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->
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creating
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copying
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->
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copying
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->
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->
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copying
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->
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copying
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->
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->
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copying
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creating
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copying
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copying
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to magic.cpython-37.pyc
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to version.cpython-37.pyc
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to __init__.cpython-37.pyc
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to mpi.cpython-37.pyc
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to dataset.cpython-37.pyc
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to base.cpython-37.pyc
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to multiprocess.cpython-37.pyc
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to __init__.cpython-37.pyc
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to build.cpython-37.pyc
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to __init__.cpython-37.pyc
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to __init__.cpython-37.pyc
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to view.cpython-37.pyc
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to __init__.cpython-37.pyc
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to serialize.cpython-37.pyc
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to __init__.cpython-37.pyc
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to nucleic_acid_analysis.cpython-37.pyc
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to vector.cpython-37.pyc
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to __init__.cpython-37.pyc
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to analysis_dict.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/analysis/energy_analysis.py
to energy_analysis.cpython-37.pyc
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to __init__.cpython-37.pyc
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to nmr.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/analysis/rmsd.py
to rmsd.cpython-37.pyc
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to water.cpython-37.pyc
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to __init__.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/analysis/base_holder.py
to base_holder.cpython-37.pyc
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to topology_analysis.cpython-37.pyc
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to dssp_analysis.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/analysis/matrix.py
to matrix.cpython-37.pyc
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to hbond_analysis.cpython-37.pyc
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to dihedral_analysis.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/cluster/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/sandbox/transform.py
to transform.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/sandbox/qm.py
to qm.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/sandbox/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/sandbox/lazy.py
to lazy.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/sandbox/TrajectoryBaseIterator.py
to TrajectoryBaseIterator.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/decorators.py
to decorators.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/Timer.py
to Timer.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/c_commands.py
to c_commands.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/get_common_objects.py
to get_common_objects.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/convert.py
to convert.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/context.py
to context.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/tools.py
to tools.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/check_and_assert.py
to check_and_assert.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/misc.py
to misc.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/utils/progress.py
to progress.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/all_actions.py
to all_actions.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/datasets/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/datasets/datasetlist.py
to datasetlist.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/datasets/array.py
to array.cpython-37.pyc
byte-compiling
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to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/core/elements.py
to elements.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/trajectory/trajectory_iterator.py
to trajectory_iterator.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/trajectory/shared_trajectory.py
to shared_trajectory.cpython-37.pyc
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to __init__.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/trajectory/trajectory.py
to trajectory.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/trajectory/c_traj/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/trajectory/stripped_trajectory.py
to stripped_trajectory.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg/pytraj/trajectory/frameiter.py
to frameiter.cpython-37.pyc
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to shared_methods.cpython-37.pyc
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to __init__.cpython-37.pyc
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to __init__.cpython-37.pyc
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to __init__.cpython-37.pyc
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to __init__.cpython-37.pyc
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to load_samples.cpython-37.pyc
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to __init__.cpython-37.pyc
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to __init__.cpython-37.pyc
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to io.cpython-37.pyc
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to __init__.cpython-37.pyc
creating stub loader for pytraj/topology/
topology.cpython-37m-x86_64-linux-gnu.so
creating stub loader for pytraj/analysis/c_analysis/
c_analysis.cpython-37m-x86_64-linux-gnu.so
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c_action.cpython-37m-x86_64-linux-gnu.so
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topology_objects.cpython-37m-x86_64-linux-gnu.so
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parameter_types.cpython-37m-x86_64-linux-gnu.so
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frame.cpython-37m-x86_64-linux-gnu.so
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c_trajectory.cpython-37m-x86_64-linux-gnu.so
creating stub loader for pytraj/trajectory/c_traj/
c_trajout.cpython-37m-x86_64-linux-gnu.so
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cpp_math.cpython-37m-x86_64-linux-gnu.so
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to topology.cpython-37.pyc
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to c_analysis.cpython-37.pyc
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to actionlist.cpython-37.pyc
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to c_datasetlist.cpython-37.pyc
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to cpp_math.cpython-37.pyc
creating
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copying pytraj.egg-info/PKG-INFO ->
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writing
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pytraj.__pycache__.__init__.cpython-37: module references __file__
pytraj.analysis.c_action.__pycache__.actionlist.cpython-37: module
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pytraj.analysis.c_action.__pycache__.c_action.cpython-37: module references
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pytraj.analysis.c_analysis.__pycache__.c_analysis.cpython-37: module
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pytraj.core.__pycache__.box.cpython-37: module references __file__
pytraj.core.__pycache__.c_core.cpython-37: module references __file__
pytraj.core.__pycache__.c_dict.cpython-37: module references __file__
pytraj.core.__pycache__.c_options.cpython-37: module references __file__
pytraj.core.__pycache__.coordinfo.cpython-37: module references __file__
pytraj.core.__pycache__.parameter_types.cpython-37: module references
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pytraj.core.__pycache__.topology_objects.cpython-37: module references
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pytraj.datafiles.__pycache__.__init__.cpython-37: module references __file__
pytraj.datafiles.__pycache__.datafiles.cpython-37: module references
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pytraj.datafiles.__pycache__.load_samples.cpython-37: module references
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pytraj.datasets.__pycache__.c_datasetlist.cpython-37: module references
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pytraj.datasets.__pycache__.c_datasets.cpython-37: module references
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pytraj.datasets.__pycache__.cast_dataset.cpython-37: module references
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pytraj.math.__pycache__.cpp_math.cpython-37: module references __file__
pytraj.testing.__pycache__.testing.cpython-37: module references __file__
pytraj.topology.__pycache__.topology.cpython-37: module references __file__
pytraj.trajectory.__pycache__.frame.cpython-37: module references __file__
pytraj.trajectory.c_traj.__pycache__.c_trajectory.cpython-37: module
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pytraj.trajectory.c_traj.__pycache__.c_trajout.cpython-37: module
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pytraj.utils.__pycache__.__init__.cpython-37: module references __path__
pytraj.utils.__pycache__.cyutils.cpython-37: module references __file__
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inspect.getsource
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creating 'dist/pytraj-2.0.5-py3.7-linux-x86_64.egg' and adding
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to it
removing
'/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/bdist.linux-x86_64/egg'
(and everything under it)
Processing pytraj-2.0.5-py3.7-linux-x86_64.egg
removing
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(and everything under it)
creating
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Extracting pytraj-2.0.5-py3.7-linux-x86_64.egg to
/home/sks/Desktop/SUCHETANA/amber20/lib/python3.7/site-packages
pytraj 2.0.5 is already the active version in easy-install.pth
Installed
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Processing dependencies for pytraj==2.0.5
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/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/lib/pdb4amber/residue.py
->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/lib/pdb4amber/utils.py
->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber/pdb4amber.py
to pdb4amber.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber/template.py
to template.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber/leap_runner.py
to leap_runner.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber/residue.py
to residue.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/pdb4amber/utils.py
to utils.cpython-37.pyc
creating
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/EGG-INFO
copying pdb4amber.egg-info/PKG-INFO ->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/EGG-INFO
copying pdb4amber.egg-info/SOURCES.txt ->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/EGG-INFO
copying pdb4amber.egg-info/dependency_links.txt ->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/EGG-INFO
copying pdb4amber.egg-info/entry_points.txt ->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/EGG-INFO
copying pdb4amber.egg-info/not-zip-safe ->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/EGG-INFO
copying pdb4amber.egg-info/top_level.txt ->
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/pdb4amber-1.7.dev0-py3.7.egg' and adding
'/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg'
to it
removing
'/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/pdb4amber/CMakeFiles/python-build/bdist.linux-x86_64/egg'
(and everything under it)
Processing pdb4amber-1.7.dev0-py3.7.egg
removing
'/home/sks/Desktop/SUCHETANA/amber20/lib/python3.7/site-packages/pdb4amber-1.7.dev0-py3.7.egg'
(and everything under it)
creating
/home/sks/Desktop/SUCHETANA/amber20/lib/python3.7/site-packages/pdb4amber-1.7.dev0-py3.7.egg
Extracting pdb4amber-1.7.dev0-py3.7.egg to
/home/sks/Desktop/SUCHETANA/amber20/lib/python3.7/site-packages
pdb4amber 1.7.dev0 is already the active version in easy-install.pth
Installing pdb4amber script to /home/sks/Desktop/SUCHETANA/amber20/bin
Installed
/home/sks/Desktop/SUCHETANA/amber20/lib/python3.7/site-packages/pdb4amber-1.7.dev0-py3.7.egg
Processing dependencies for pdb4amber==1.7.dev0
Finished processing dependencies for pdb4amber==1.7.dev0
/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.7/site-packages/setuptools/dist.py:454:
UserWarning: Normalizing '1.7.dev' to '1.7.dev0'
  warnings.warn(tmpl.format(**locals()))
Inside Amber CMake build system, skipping build of native executables
running build
running build_py
running egg_info
writing packmol_memgen.egg-info/PKG-INFO
writing dependency_links to packmol_memgen.egg-info/dependency_links.txt
writing requirements to packmol_memgen.egg-info/requires.txt
writing top-level names to packmol_memgen.egg-info/top_level.txt
reading manifest file 'packmol_memgen.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'packmol_memgen.egg-info/SOURCES.txt'
running build_scripts
running install
running install_lib
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/example/example.sh
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/example
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/data/CLI.lib
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/data/pdbs.tar.gz
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/data/frcmod.lipid17_ext
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/data/lipid17_lyso.lib
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/data/leaprc.lipid17_ext
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/data/lipid17_pips.lib
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/data/memgen.parm
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/__version__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/charmmlipid2amber/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/charmmlipid2amber
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/charmmlipid2amber
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/charmmlipid2amber
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/protein.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/trajectory.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix
copying
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->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/pymol.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/fetch.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/hydroxide.lib
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/aminoacid.pdb
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/phd.leaprc
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/template.pdb
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/phd.frcmod
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/znb.leaprc
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/opls.parameter
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/color_b.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/opls.topology
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/hin.lib
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
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->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/phd.prepin
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/znb.frcmod
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/make_chi.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/znb.lib
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/charmm22.topology
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/data/binaries.json
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/pdbremix/util.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix
copying
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->
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->
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->
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copying
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->
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->
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copying
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->
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->
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->
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->
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->
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->
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->
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/memembed
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/memembed/Makefile
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/memembed
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/memembed/README
->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/measure_parms.py
->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/amber.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/_tqdm.py
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->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/__init__.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/tests/tests_pandas.py
->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/tests/tests_version.py
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/tests/tests_tqdm.py
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/tests/tests_perf.py
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/tests
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/tests/tests_main.py
->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/__main__.py
->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/_utils.py
->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/_main.py
->
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copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/_tqdm_pandas.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/_version.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/lib/tqdm/_tqdm_gui.py
->
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/lib/packmol_memgen/Makefile
->
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copying
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->
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byte-compiling
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to __init__.cpython-37.pyc
byte-compiling
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to __version__.cpython-37.pyc
byte-compiling
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to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/charmmlipid2amber/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py
to charmmlipid2amber.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/protein.py
to protein.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data.py
to data.cpython-37.pyc
byte-compiling
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to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/trajectory.py
to trajectory.cpython-37.pyc
byte-compiling
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to rmsd.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/pymol.py
to pymol.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/fetch.py
to fetch.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data/color_b.py
to color_b.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/data/make_chi.py
to make_chi.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/util.py
to util.cpython-37.pyc
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/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/v3numpy.py
to v3numpy.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/volume.py
to volume.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/lib/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/lib/docopt.py
to docopt.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/lib/pyqcprot.py
to pyqcprot.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py
to pdbatoms.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/pdbtext.py
to pdbtext.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/v3.py
to v3.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/spacehash.py
to spacehash.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/amber.py
to amber.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/_version.py
to _version.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/simulate.py
to simulate.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/namd.py
to namd.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/force.py
to force.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/v3array.py
to v3array.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/gromacs.py
to gromacs.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/pdbremix/asa.py
to asa.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/memembed/scripts/pymol_rotate.py
to pymol_rotate.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/memembed/scripts/pymol_membrane_image.py
to pymol_membrane_image.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/measure_parms.py
to measure_parms.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/amber.py
to amber.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/_tqdm.py
to _tqdm.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/_tqdm_notebook.py
to _tqdm_notebook.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/__init__.py
to __init__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/tests/tests_pandas.py
to tests_pandas.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/tests/tests_version.py
to tests_version.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/tests/tests_tqdm.py
to tests_tqdm.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/tests/tests_perf.py
to tests_perf.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/tests/tests_main.py
to tests_main.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/__main__.py
to __main__.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/_utils.py
to _utils.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/_main.py
to _main.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/_tqdm_pandas.py
to _tqdm_pandas.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/_version.py
to _version.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/lib/tqdm/_tqdm_gui.py
to _tqdm_gui.cpython-37.pyc
byte-compiling
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen/main.py
to main.cpython-37.pyc
running install_egg_info
removing
'/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen-1.1.0rc0-py3.7.egg-info'
(and everything under it)
Copying packmol_memgen.egg-info to
/home/sks/Desktop/SUCHETANA/amber20//lib/python3.7/site-packages/packmol_memgen-1.1.0rc0-py3.7.egg-info
running install_scripts
copying
/home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/packmol_memgen/CMakeFiles/python-build/scripts-3.7/packmol-memgen
-> /home/sks/Desktop/SUCHETANA/amber20/bin
changing mode of /home/sks/Desktop/SUCHETANA/amber20/bin/packmol-memgen to
755
/home/sks/Desktop/SUCHETANA/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.7/site-packages/setuptools/dist.py:454:
UserWarning: Normalizing '1.1.0.rc' to '1.1.0rc0'
  warnings.warn(tmpl.format(**locals()))
-- Installing:
/home/sks/Desktop/SUCHETANA/amber20/test//./cuda/gbsa_xfin/gbsa3in
-- Fixing Miniconda script shebangs
Thanks
Suchetana Gupta
IACS, Kolkata
On Mon, Jun 29, 2020 at 11:35 PM David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Jun 29, 2020, Suchetana Gupta wrote:
>
> >We tried installing Amber 20 on our GPU machine. While the serial
> >installation was smooth, we could not install it on GPU.
>
> Did you modify the run_cmake script to set -DCUDA=TRUE?  Your build
> report from cmake indicates that CUDA is OFF, so it never even tried to
> build pmemd.cuda.
>
> All the tests then fail with simple messages like this:
>
> /home/sks/Desktop/SUCHETANA/amber20/bin/pmemd.cuda_DPFP: Command not found.
>
> This is consistent with the hypothesis that you never asked to build
> pmemd.cuda.  But there may be something else happening that I'm not
> seeing -- better to post your log file as a text file, rather than
> converting it to Microsoft Word....
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 29 2020 - 21:00:03 PDT