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!