make[2]: Entering directory `/state/partition1/apps/amber12/AmberTools/test' ./test_at_clean.sh cd mmpbsa_py && make -k clean make[3]: Entering directory `/state/partition1/apps/amber12/AmberTools/test/mmpbsa_py' cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif cd 01_Generalized_Born && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 02_Poisson_Boltzmann && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 03_Alanine_Scanning && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 04_Per_Residue_Decomp && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 05_Pairwise_Decomp && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 06_NAB_Nmode && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 07_Comprehensive && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 08_Stability && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 09_APBS_Poisson_Boltzmann && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 10_QM_MMGBSA && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) cd 11_3D-RISM && /export/apps/amber12//bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv /bin/sh: /export/apps/amber12//bin/MMPBSA.py: No such file or directory make[3]: [clean] Error 127 (ignored) make[3]: Leaving directory `/state/partition1/apps/amber12/AmberTools/test/mmpbsa_py' cd cpptraj && make -k clean make[3]: Entering directory `/state/partition1/apps/amber12/AmberTools/test/cpptraj' 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 OPT=clean make[4]: Entering directory `/state/partition1/apps/amber12/AmberTools/test/cpptraj' make[4]: Leaving directory `/state/partition1/apps/amber12/AmberTools/test/cpptraj' make[3]: Leaving directory `/state/partition1/apps/amber12/AmberTools/test/cpptraj' cd leap/glycam && ./Run_tests.bash clean cd nab && make -k test make[3]: Entering directory `/state/partition1/apps/amber12/AmberTools/test/nab' Running test to do simple minimization (this tests the molecular mechanics interface) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.sff: Program error make[3]: *** [sff_test] Error 1 Running test to do simple minimization with shake (this tests the molecular mechanics interface) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.shake: Program error make[3]: *** [rattle_min_test] Error 1 Running test to do simple minimization (this tests the generalized Born implementation) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.gb: Program error make[3]: *** [gb_test] Error 1 Running test to do simple minimization (this tests the generalized Born implementation) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.xfin: Program error make[3]: *** [xfin_test] Error 1 Running test to do simple minimization (this tests the LCPO surface area) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.gbsa: Program error make[3]: *** [gbsa_test] Error 1 Running test to do simple minimization (this tests the ao generalized Born implementation) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.gb2: Program error make[3]: *** [gb2_test] Error 1 Running test to do simple minimization (this tests the ao-2 generalized Born implementation) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.gb5: Program error make[3]: *** [gb5_test] Error 1 Running test to do simple minimization (this tests the GB Neck implementation; gb==8) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.gb8: Program error make[3]: *** [gb8_test] Error 1 Running test to do simple minimization (this tests the GB Neck implementation; gb==7) /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.gb7: Program error make[3]: *** [gb7_test] Error 1 Running test to do molecular dynamics with rattle /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.rattle_md: Program error make[3]: *** [rattle_md_test] Error 1 Running test to compute NAB energy of 3dfr minus waters. /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.dhfrndpmtx: Program error make[3]: *** [dhfrndpmtx_test] Error 1 Running test to compute GB Newton-Raphson and normal modes: /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.asp: Program error make[3]: *** [asp_test] Error 1 Running test to compute non-GB Newton-Raphson and normal modes: /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.aspnb: Program error make[3]: *** [aspnb_test] Error 1 Running test to create Amber force-field description /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.prm: Program error make[3]: *** [prm_test] Error 1 Running test to do simple xmin minimization /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.xmin: Program error make[3]: *** [xmin_test] Error 1 Running test on netcdf files /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.netcdf: Program error make[3]: *** [netcdf_test] Error 1 Running test for variable 1-4 scaled nonbonded interactions /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.variable_14: Program error make[3]: *** [variable_14test] Error 1 Running test to do simple lmod optimization /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.lmod: Program error make[3]: *** [lmod_test] Error 1 Running test to compute GB normal modes using DSYEVD: /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.nmode1: Program error make[3]: *** [nmode1_test] Error 1 Running test to compute GB normal modes using DSAUPD: /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.nmode2: Program error make[3]: *** [nmode2_test] Error 1 Running test to compute Langevin modes: /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./Run.nmode3: Program error make[3]: *** [nmode3_test] Error 1 Running test of the isotropic periodic sum technique /usr/bin/ld: cannot find -lcifparse collect2: ld returned 1 exit status cc failed! ./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 `/state/partition1/apps/amber12/AmberTools/test/nab' make[2]: *** [test.nab] Error 2 cd mmpbsa_py && make test make[3]: Entering directory `/state/partition1/apps/amber12/AmberTools/test/mmpbsa_py' cd EstRAL_Files && ./Run.makeparms This is not a parallel test. cd 01_Generalized_Born && ./Run.GB Cannot have more than 2 processors for this test. cd 02_Poisson_Boltzmann && ./Run.PB Cannot have more than 2 processors for this test. cd 03_Alanine_Scanning && ./Run.ALA Cannot have more than 2 processors for this test. cd 04_Per_Residue_Decomp && ./Run.PerRes This test requires sander and can only be run with Amber12 installed. cd 05_Pairwise_Decomp && ./Run.Pairwise This test requires sander and can only be run with Amber12 installed. cd 06_NAB_Nmode && ./Run.nmode Cannot have more than 2 processors for this test. cd 07_Comprehensive && ./Run.comprehensive This test requires sander and can only be run with Amber12 installed. cd 08_Stability && ./Run.stability This test requires sander and can only be run with Amber12 installed. cd 10_QM_MMGBSA && ./Run.QMMMGBSA This test requires sander and can only be run with Amber12 installed. cd 11_3D-RISM && ./Run.rism3d Cannot find /export/apps/amber12//bin/rism3d.snglpnt. Cannot run this test. make[3]: Leaving directory `/state/partition1/apps/amber12/AmberTools/test/mmpbsa_py' Finished test suite for AmberTools at Sat Dec 10 13:25:30 IST 2016. make[2]: Target `test.parallel2' not remade because of errors. make[2]: Leaving directory `/state/partition1/apps/amber12/AmberTools/test' 0 file comparisons passed 0 file comparisons failed 56 tests experienced errors Test log file saved as /export/apps/amber12//logs/test_at_parallel/2016-12-10_13-25-24.log No test diffs to save!