have you "make install" after doing the configuration yet?
e.g:
./configure -mpi gnu
make install
Hai
On Tue, Jul 25, 2017 at 5:10 AM, Debasish Mandal <debu1500.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jul 25 2017 - 06:00:07 PDT
