Dear Amber Users,
I am Installing AmberTools 17 in my
machine. The installation is sucessful. But when I am trying to configure
with openmpi and use the command make test after export DO_PARALLEL=”mpirun
-np 8” but it is terminated with the following error.
(cd AmberTools/test && make test.openmp)
make[1]: Entering directory `/home/program/amber16/AmberTools/test'
./test_at_openmp.sh
make[2]: Entering directory `/home/program/amber16/AmberTools/test'
./test_at_clean.sh
cd antechamber && make -k clean
make[3]: Entering directory
`/home/program/amber16/AmberTools/test/antechamber'
Cleaning all antechamber test subdirectories:
find . -name "*.dif" -print0 | xargs -0 /bin/rm -f
/bin/rm -f \
ash/antechamber.out \
ash/sqm.in \
ash/sqm.out \
ash/sqm.pdb \
bondtype/antechamber.out \
c60/antechamber.out \
charmm/antechamber.out \
fluorescein/antechamber.out \
fluorescein/sqm.in \
fluorescein/sqm.out \
fpph/antechamber.out \
guanine_amber/antechamber.out \
guanine_amber/sqm.in \
guanine_amber/sqm.out \
guanine_amber/sqm.pdb \
residuegen/ala_conf1.esp \
residuegen/ala_conf2.esp \
residuegen/ANTECHAMBER_AC.AC \
residuegen/ANTECHAMBER_AC.AC0 \
residuegen/ANTECHAMBER_BOND_TYPE.AC \
residuegen/ANTECHAMBER_BOND_TYPE.AC0 \
residuegen/antechamber.out \
residuegen/ATOMTYPE.INF \
residuegen/esout \
residuegen/espgen.out \
residuegen/NEWPDB.PDB \
residuegen/PREP.INF \
residuegen/punch \
residuegen/QIN \
residuegen/qout \
residuegen/RESIDUE_GEN_MAINCHAIN.DAT \
residuegen/RESIDUE_GEN_RESP.INPUT1 \
residuegen/RESIDUE_GEN_RESP.INPUT2 \
residuegen/RESIDUE_GEN_RESP.OUTPUT1 \
residuegen/RESIDUE_GEN_RESP.OUTPUT2 \
residuegen/RESIDUE_GEN_RESPGEN.DAT \
residuegen/RESIDUE_GEN.AC \
residuegen/residuegen.out \
sustiva/antechamber.out \
sustiva/leap.log \
sustiva/prmtop \
sustiva/sqm.in \
sustiva/sqm.out \
tp/antechamber.out \
tp/sqm.out
make[3]: Leaving directory
`/home/program/amber16/AmberTools/test/antechamber'
cd mmpbsa_py && make -k clean
make[3]: Entering directory
`/home/program/amber16/AmberTools/test/mmpbsa_py'
cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif
cd 01_Generalized_Born && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat
*.dif *.csv
cd 02_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat
*.dif *.csv
cd 03_Alanine_Scanning && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat
*.dif *.csv
cd 04_Per_Residue_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.*
FINAL_*_MMPBSA.dat *.dif *.csv
cd 05_Pairwise_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat
*.dif *.csv
cd 06_NAB_Nmode && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif
*.csv
cd 07_Comprehensive && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat
*.dif *.csv
cd 08_Stability && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif
*.csv
cd 09_APBS_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.*
FINAL_*_MMPBSA.dat *.dif *.csv
cd 10_QM_MMGBSA && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif
*.csv
cd 11_3D-RISM && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif
*.csv
cd 12_Membrane_Channel && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat
*.dif *.csv
make[3]: Leaving directory `/home/program/amber16/AmberTools/test/mmpbsa_py'
cd /home/program/amber16/AmberTools/src/mm_pbsa/Examples &&
./Run.mmpbsa.clean
cd /home/program/amber16/AmberTools/src/FEW/examples/test && ./Run.few.clean
cd /home/program/amber16/AmberTools/src/cpptraj/test && make -k clean
make[3]: Entering directory
`/home/program/amber16/AmberTools/src/cpptraj/test'
Cleaning all test directories:
(find . -name 'test.out' -o -name 'valgrind.out' -o -name 'Thread.*' \
-o -name 'Test_Results.dat' -o -name 'Test_Error.dat' | \
while read dif ;\
do \
rm -f $dif ;\
done ;\
)
make test.complete test.libcpptraj OPT=clean
make[4]: Entering directory
`/home/program/amber16/AmberTools/src/cpptraj/test'
make[4]: Leaving directory
`/home/program/amber16/AmberTools/src/cpptraj/test'
make[3]: Leaving directory
`/home/program/amber16/AmberTools/src/cpptraj/test'
cd leap && make -k clean
make[3]: Entering directory `/home/program/amber16/AmberTools/test/leap'
Cleaning all test directories:
(find . -name 'leap.log' -o -name 'leap.out' | \
while read dif ;\
do \
rm -f $dif ;\
done ;\
)
make test.complete OPT=clean
make[4]: Entering directory `/home/program/amber16/AmberTools/test/leap'
make[4]: Leaving directory `/home/program/amber16/AmberTools/test/leap'
make[3]: Leaving directory `/home/program/amber16/AmberTools/test/leap'
cd leap/glycam/06j && ./Run.glycam clean
cd leap/glycam/06EPb && ./Run.glycam clean
cd leap/glycam/06j_10 && ./Run.glycam clean
cd leap/glycam/06j_12SB && ./Run.glycam clean
cd nab && make -k test
make[3]: Entering directory `/home/program/amber16/AmberTools/test/nab'
Running test to do simple minimization
(this tests the molecular mechanics interface)
./Run.sff: 14: ./Run.sff: /home/program/amber16/bin/mpinab: not found
./Run.sff: Program error
make[3]: *** [sff_test] Error 1
Running test to do simple minimization with shake
(this tests the molecular mechanics interface)
./Run.shake: 14: ./Run.shake: /home/program/amber16/bin/mpinab: not found
./Run.shake: Program error
make[3]: *** [rattle_min_test] Error 1
Running test to do simple minimization
(this tests the generalized Born implementation)
./Run.gb: 14: ./Run.gb: /home/program/amber16/bin/mpinab: not found
./Run.gb: Program error
make[3]: *** [gb_test] Error 1
Running test to do simple minimization
(this tests the generalized Born implementation)
./Run.xfin: 14: ./Run.xfin: /home/program/amber16/bin/mpinab: not found
./Run.xfin: Program error
make[3]: *** [xfin_test] Error 1
Running test to do simple minimization
(this tests the LCPO surface area)
./Run.gbsa: 14: ./Run.gbsa: /home/program/amber16/bin/mpinab: not found
./Run.gbsa: Program error
make[3]: *** [gbsa_test] Error 1
Running test to do simple minimization
(this tests the ao generalized Born implementation)
./Run.gb2: 14: ./Run.gb2: /home/program/amber16/bin/mpinab: not found
./Run.gb2: Program error
make[3]: *** [gb2_test] Error 1
Running test to do simple minimization
(this tests the ao-2 generalized Born implementation)
./Run.gb5: 14: ./Run.gb5: /home/program/amber16/bin/mpinab: not found
./Run.gb5: Program error
make[3]: *** [gb5_test] Error 1
Running test to do simple minimization
(this tests the GB Neck implementation; gb==8)
./Run.gb8: 14: ./Run.gb8: /home/program/amber16/bin/mpinab: not found
./Run.gb8: Program error
make[3]: *** [gb8_test] Error 1
Running test to do simple minimization
(this tests the GB Neck implementation; gb==7)
./Run.gb7: 14: ./Run.gb7: /home/program/amber16/bin/mpinab: not found
./Run.gb7: Program error
make[3]: *** [gb7_test] Error 1
Running test to do molecular dynamics with rattle
./Run.rattle_md: 13: ./Run.rattle_md: /home/program/amber16/bin/mpinab: not
found
./Run.rattle_md: Program error
exportmake[3]: *** [rattle_md_test] Error 1
Running test to compute NAB energy of 3dfr minus waters.
./Run.dhfrndpmtx: 13: ./Run.dhfrndpmtx: /home/program/amber16/bin/mpinab:
not found
./Run.dhfrndpmtx: Program error
make[3]: *** [dhfrndpmtx_test] Error 1
Running test to compute GB Newton-Raphson and normal modes:
./Run.asp: 13: ./Run.asp: /home/program/amber16/bin/mpinab: not found
./Run.asp: Program error
make[3]: *** [asp_test] Error 1
Running test to compute non-GB Newton-Raphson and normal modes:
./Run.aspnb: 13: ./Run.aspnb: /home/program/amber16/bin/mpinab: not found
./Run.aspnb: Program error
make[3]: *** [aspnb_test] Error 1
Running test to create Amber force-field description
./Run.prm: 13: ./Run.prm: /home/program/amber16/bin/mpinab: not found
./Run.prm: Program error
make[3]: *** [prm_test] Error 1
Running test to do simple xmin minimization
./Run.xmin: 13: ./Run.xmin: /home/program/amber16/bin/mpinab: not found
./Run.xmin: Program error
make[3]: *** [xmin_test] Error 1
Running test on netcdf files
./Run.netcdf: 13: ./Run.netcdf: /home/program/amber16/bin/mpinab: not found
./Run.netcdf: Program error
make[3]: *** [netcdf_test] Error 1
Running test for variable 1-4 scaled nonbonded interactions
./Run.variable_14: 13: ./Run.variable_14: /home/program/amber16/bin/mpinab:
not found
./Run.variable_14: Program error
make[3]: *** [variable_14test] Error 1
Running test to do simple lmod optimization
./Run.lmod: 13: ./Run.lmod: /home/program/amber16/bin/mpinab: not found
./Run.lmod: Program error
make[3]: *** [lmod_test] Error 1
Running test to compute GB normal modes using DSYEVD:
./Run.nmode1: 13: ./Run.nmode1: /home/program/amber16/bin/mpinab: not found
./Run.nmode1: Program error
make[3]: *** [nmode1_test] Error 1
Running test to compute GB normal modes using DSAUPD:
./Run.nmode2: 13: ./Run.nmode2: /home/program/amber16/bin/mpinab: not found
./Run.nmode2: Program error
make[3]: *** [nmode2_test] Error 1
Running test to compute Langevin modes:
./Run.nmode3: 13: ./Run.nmode3: /home/program/amber16/bin/mpinab: not found
./Run.nmode3: Program error
make[3]: *** [nmode3_test] Error 1
Running test of the isotropic periodic sum technique
./Run.ips: 13: ./Run.ips: /home/program/amber16/bin/mpinab: not found
./Run.ips: Program error
make[3]: *** [ips_test] Error 1
Running test to do simple minimization (libpbsa)
(this tests the PBSA implementation)
Please note that PARALLEL PBSA is not implemented in nab.
============================================================================
make[3]: Target `test' not remade because of errors.
make[3]: Leaving directory `/home/program/amber16/AmberTools/test/nab'
make[2]: *** [test.openmp2] Error 2
make[2]: Leaving directory `/home/program/amber16/AmberTools/test'
make[2]: Entering directory `/home/program/amber16/AmberTools/test'
Finished test suite for AmberTools at Tue Jul 25 14:35:03 IST 2017.
make[2]: Leaving directory `/home/program/amber16/AmberTools/test'
0 file comparisons passed
0 file comparisons failed
22 tests experienced errors
Test log file saved as
/home/program/amber16/logs/test_at_openmp/2017-07-25_14-35-02.log
No test diffs to save!
make[1]: Leaving directory `/home/program/amber16/AmberTools/test'
Could you please help to solve this problem? Your help will be highly
appreciated.
Thanks in advance
Debasish
======================================
Debasish Mandal
Post Doctoral Research Fellow
C/o- Prof. Sason Shaik
Institute of Chemistry
The Hebrew University of Jerusalem,
Givat Ram Campus,
Jerusalem, 91904, Israel
E-mail: debu1500.gmail.com
Mob.No-08017296958
“I’m thankful to all those who said ‘NO’ to me it's because of them, I did it
myself” Einstein
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Received on Tue Jul 25 2017 - 02:30:03 PDT
