Dear Amber Fans
The installation of amber24 in ubuntu 24.04 ran well. The test of parallel
installation gives the following
make[2]: Entering directory '/home/ibrahim/amber24/AmberTools/test'
./test_at_clean.sh
cd antechamber && make -k clean
make[3]: Entering directory
'/home/ibrahim/amber24/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/ibrahim/amber24/AmberTools/test/antechamber'
cd mmpbsa_py && make -k clean
make[3]: Entering directory
'/home/ibrahim/amber24/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
cd 13_Auto_membrane && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat
*.dif *.csv
cd 14_MultiTraj_Membrane && /bin/rm -f _MMPBSA_* mmpbsa.*
FINAL_*_MMPBSA.dat *.dif *.csv
make[3]: Leaving directory '/home/ibrahim/amber24/AmberTools/test/mmpbsa_py'
cd ../src/mm_pbsa/Examples && ./Run.mmpbsa.clean
cd ../src/FEW/examples/test && ./Run.few.clean
cd ../src/cpptraj/test && make -k clean
make[3]: Entering directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
Cleaning all test directories:
make test.complete test.libcpptraj OPT=clean
make[4]: Entering directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
make[5]: Entering directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
make[5]: Leaving directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
make[4]: Leaving directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
make[3]: Leaving directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
cd leap && make -k clean
make[3]: Entering directory '/home/ibrahim/amber24/AmberTools/test/leap'
Cleaning all test directories:
(find . -name "*.dif" -o -name 'leap.log' -o -name 'leap.out' | \
while read dif ;\
do \
rm -f $dif ;\
done ;\
)
/bin/rm -f x.lib lib94.out ions94.log ff94_prm.out ff94_prm.log ff94.log
make test.params OPT=clean
make[4]: Entering directory '/home/ibrahim/amber24/AmberTools/test/leap'
make[4]: Leaving directory '/home/ibrahim/amber24/AmberTools/test/leap'
make[3]: Leaving directory '/home/ibrahim/amber24/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 ../src/cpptraj/test && make -k test
make[3]: Entering directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
make test.complete summary
make[4]: Entering directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
Error: Required binary 'ncdump' not found.
make[4]: *** [Makefile:733: test.complete] Error 1
Error: Required binary 'ncdump' not found.
make[4]: *** [Makefile:741: summary] Error 1
make[4]: Leaving directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
make[3]: *** [Makefile:715: test.all] Error 2
make[3]: Target 'test' not remade because of errors.
make[3]: Leaving directory
'/home/ibrahim/amber24/AmberTools/src/cpptraj/test'
make[2]: *** [Makefile:145: test.cpptraj] Error 2
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_sp_fast; fi
Running test to do basic MD (librism)
(trajectory processing using the 3D-RISM command line interface)
mpirun -np 4 /home/ibrahim/amber24///bin/rism3d.snglpnt.MPI
diffing rism3d.snglpnt.np4.fast.out.check.totChg with
rism3d.snglpnt.np4.fast.out.totChg
PASSED
==============================================================
diffing rism3d.snglpnt.np4.fast.out.check.rel with
rism3d.snglpnt.np4.fast.out.rel
PASSED
==============================================================
diffing quv.1.xyzv.fast.trunc.check with quv.1.xyzv.fast.trunc
PASSED
==============================================================
diffing quv.2.xyzv.fast.trunc.check with quv.2.xyzv.fast.trunc
PASSED
==============================================================
diffing quv.3.xyzv.fast.trunc.check with quv.3.xyzv.fast.trunc
PASSED
==============================================================
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_sp_list; fi
Running test for 3D-RISM closure list (librism)
(trajectory processing test)
mpirun -np 4 /home/ibrahim/amber24///bin/rism3d.snglpnt.MPI
*** buffer overflow detected ***: terminated
[Dock:298419] *** Process received signal ***
[Dock:298419] Signal: Aborted (6)
[Dock:298419] Signal code: (-6)
*** buffer overflow detected ***: terminated
[Dock:298420] *** Process received signal ***
[Dock:298420] Signal: Aborted (6)
[Dock:298420] Signal code: (-6)
*** buffer overflow detected ***: terminated
[Dock:298421] *** Process received signal ***
[Dock:298421] Signal: Aborted (6)
[Dock:298421] Signal code: (-6)
*** buffer overflow detected ***: terminated
[Dock:298422] *** Process received signal ***
[Dock:298422] Signal: Aborted (6)
[Dock:298422] Signal code: (-6)
[Dock:298420] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x747969045330]
[Dock:298420] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x74796909eb2c]
[Dock:298420] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x74796904527e]
[Dock:298420] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7479690288ff]
[Dock:298420] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x7479690297b6]
[Dock:298420] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x747969136c19]
[Dock:298420] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x7479691365d4]
[Dock:298420] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x7479691381b9]
[Dock:298420] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x5d5081273eca]
[Dock:298420] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x5d5081274f68]
[Dock:298420] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x5d508126fdb9]
[Dock:298420] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x74796902a1ca]
[Dock:298420] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x74796902a28b]
[Dock:298420] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x5d50812710a5]
[Dock:298420] *** End of error message ***
[Dock:298421] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x717857e45330]
[Dock:298421] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x717857e9eb2c]
[Dock:298421] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x717857e4527e]
[Dock:298421] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x717857e288ff]
[Dock:298421] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x717857e297b6]
[Dock:298421] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x717857f36c19]
[Dock:298421] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x717857f365d4]
[Dock:298421] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x717857f381b9]
[Dock:298421] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x62fe8d72eeca]
[Dock:298421] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x62fe8d72ff68]
[Dock:298421] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x62fe8d72adb9]
[Dock:298421] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x717857e2a1ca]
[Dock:298421] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x717857e2a28b]
[Dock:298421] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x62fe8d72c0a5]
[Dock:298421] *** End of error message ***
[Dock:298422] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x76303d845330]
[Dock:298422] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x76303d89eb2c]
[Dock:298422] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x76303d84527e]
[Dock:298422] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x76303d8288ff]
[Dock:298422] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x76303d8297b6]
[Dock:298422] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x76303d936c19]
[Dock:298422] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x76303d9365d4]
[Dock:298422] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x76303d9381b9]
[Dock:298422] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x61623b82deca]
[Dock:298422] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x61623b82ef68]
[Dock:298422] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x61623b829db9]
[Dock:298422] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x76303d82a1ca]
[Dock:298422] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x76303d82a28b]
[Dock:298422] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x61623b82b0a5]
[Dock:298422] *** End of error message ***
[Dock:298419] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x78d3bba45330]
[Dock:298419] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x78d3bba9eb2c]
[Dock:298419] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x78d3bba4527e]
[Dock:298419] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x78d3bba288ff]
[Dock:298419] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x78d3bba297b6]
[Dock:298419] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x78d3bbb36c19]
[Dock:298419] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x78d3bbb365d4]
[Dock:298419] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x78d3bbb381b9]
[Dock:298419] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x595262dfdeca]
[Dock:298419] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x595262dfef68]
[Dock:298419] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x595262df9db9]
[Dock:298419] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x78d3bba2a1ca]
[Dock:298419] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x78d3bba2a28b]
[Dock:298419] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x595262dfb0a5]
[Dock:298419] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 0 on node Dock exited on signal
6 (Aborted).
--------------------------------------------------------------------------
./Run.rism_sp_list: Program error
make[2]: [Makefile:337: test.rism3d.open] Error 1 (ignored)
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_sp2; fi
DO_PARALLEL set to mpirun -np 4
./Run.rism_sp2: This test runs with one process only
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_sp_astol_fast; fi
DO_PARALLEL set to mpirun -np 4
./Run.rism_sp_astol_fast: This test requires 1 or 2 processes
for meaningful comparison.
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_selftest_hnc; fi
Running test to do basic MD (librism)
(trajectory processing using the 3D-RISM command line interface)
mpirun -np 4 /home/ibrahim/amber24///bin/rism3d.snglpnt.MPI
*** buffer overflow detected ***: terminated
[Dock:298476] *** Process received signal ***
[Dock:298476] Signal: Aborted (6)
[Dock:298476] Signal code: (-6)
[Dock:298476] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x71c5d7845330]
[Dock:298476] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x71c5d789eb2c]
[Dock:298476] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x71c5d784527e]
[Dock:298476] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x71c5d78288ff]
[Dock:298476] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x71c5d78297b6]
[Dock:298476] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x71c5d7936c19]
[Dock:298476] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x71c5d79365d4]
[Dock:298476] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x71c5d79381b9]
[Dock:298476] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x62105c8d5eca]
[Dock:298476] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x62105c8d6f68]
[Dock:298476] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x62105c8d1db9]
[Dock:298476] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x71c5d782a1ca]
[Dock:298476] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x71c5d782a28b]
[Dock:298476] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x62105c8d30a5]
[Dock:298476] *** End of error message ***
*** buffer overflow detected ***: terminated
[Dock:298477] *** Process received signal ***
[Dock:298477] Signal: Aborted (6)
[Dock:298477] Signal code: (-6)
[Dock:298477] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x78d807e45330]
[Dock:298477] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x78d807e9eb2c]
[Dock:298477] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x78d807e4527e]
[Dock:298477] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x78d807e288ff]
[Dock:298477] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x78d807e297b6]
[Dock:298477] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x78d807f36c19]
[Dock:298477] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x78d807f365d4]
[Dock:298477] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x78d807f381b9]
[Dock:298477] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x5dae4ff70eca]
[Dock:298477] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x5dae4ff71f68]
[Dock:298477] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x5dae4ff6cdb9]
[Dock:298477] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x78d807e2a1ca]
[Dock:298477] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x78d807e2a28b]
[Dock:298477] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x5dae4ff6e0a5]
[Dock:298477] *** End of error message ***
*** buffer overflow detected ***: terminated
[Dock:298478] *** Process received signal ***
[Dock:298478] Signal: Aborted (6)
[Dock:298478] Signal code: (-6)
[Dock:298478] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x741186045330]
[Dock:298478] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x74118609eb2c]
[Dock:298478] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x74118604527e]
[Dock:298478] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7411860288ff]
[Dock:298478] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x7411860297b6]
[Dock:298478] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x741186136c19]
[Dock:298478] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x7411861365d4]
[Dock:298478] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x7411861381b9]
[Dock:298478] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x64378a642eca]
[Dock:298478] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x64378a643f68]
[Dock:298478] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x64378a63edb9]
[Dock:298478] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x74118602a1ca]
[Dock:298478] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x74118602a28b]
[Dock:298478] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x64378a6400a5]
[Dock:298478] *** End of error message ***
*** buffer overflow detected ***: terminated
[Dock:298479] *** Process received signal ***
[Dock:298479] Signal: Aborted (6)
[Dock:298479] Signal code: (-6)
[Dock:298479] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x799ff2845330]
[Dock:298479] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x799ff289eb2c]
[Dock:298479] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x799ff284527e]
[Dock:298479] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x799ff28288ff]
[Dock:298479] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x799ff28297b6]
[Dock:298479] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x799ff2936c19]
[Dock:298479] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x799ff29365d4]
[Dock:298479] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x799ff29381b9]
[Dock:298479] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x5632e51d6eca]
[Dock:298479] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x5632e51d7f68]
[Dock:298479] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x5632e51d2db9]
[Dock:298479] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x799ff282a1ca]
[Dock:298479] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x799ff282a28b]
[Dock:298479] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x5632e51d40a5]
[Dock:298479] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 0 on node Dock exited on signal
6 (Aborted).
--------------------------------------------------------------------------
./Run.rism_selftest_hnc: Program error
make[2]: [Makefile:340: test.rism3d.open] Error 1 (ignored)
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_selftest_kh; fi
Running test to do basic MD (librism)
(trajectory processing using the 3D-RISM command line interface)
mpirun -np 4 /home/ibrahim/amber24///bin/rism3d.snglpnt.MPI
*** buffer overflow detected ***: terminated
[Dock:298516] *** Process received signal ***
[Dock:298516] Signal: Aborted (6)
[Dock:298516] Signal code: (-6)
[Dock:298516] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x7699e9a45330]
[Dock:298516] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x7699e9a9eb2c]
[Dock:298516] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x7699e9a4527e]
[Dock:298516] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7699e9a288ff]
[Dock:298516] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x7699e9a297b6]
[Dock:298516] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x7699e9b36c19]
[Dock:298516] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x7699e9b365d4]
[Dock:298516] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x7699e9b381b9]
[Dock:298516] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x64ad6f866eca]
[Dock:298516] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x64ad6f867f68]
[Dock:298516] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x64ad6f862db9]
[Dock:298516] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x7699e9a2a1ca]
[Dock:298516] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7699e9a2a28b]
[Dock:298516] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x64ad6f8640a5]
[Dock:298516] *** End of error message ***
*** buffer overflow detected ***: terminated
[Dock:298517] *** Process received signal ***
[Dock:298517] Signal: Aborted (6)
[Dock:298517] Signal code: (-6)
[Dock:298517] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x7e325ea45330]
[Dock:298517] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x7e325ea9eb2c]
[Dock:298517] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x7e325ea4527e]
[Dock:298517] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7e325ea288ff]
[Dock:298517] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x7e325ea297b6]
[Dock:298517] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x7e325eb36c19]
[Dock:298517] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x7e325eb365d4]
[Dock:298517] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x7e325eb381b9]
[Dock:298517] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x5a590d60ceca]
[Dock:298517] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x5a590d60df68]
[Dock:298517] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x5a590d608db9]
[Dock:298517] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x7e325ea2a1ca]
[Dock:298517] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7e325ea2a28b]
[Dock:298517] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x5a590d60a0a5]
[Dock:298517] *** End of error message ***
*** buffer overflow detected ***: terminated
[Dock:298518] *** Process received signal ***
[Dock:298518] Signal: Aborted (6)
[Dock:298518] Signal code: (-6)
[Dock:298518] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x76327c845330]
[Dock:298518] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x76327c89eb2c]
[Dock:298518] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x76327c84527e]
[Dock:298518] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x76327c8288ff]
[Dock:298518] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x76327c8297b6]
[Dock:298518] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x76327c936c19]
[Dock:298518] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x76327c9365d4]
[Dock:298518] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x76327c9381b9]
[Dock:298518] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x5e136663beca]
[Dock:298518] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x5e136663cf68]
[Dock:298518] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x5e1366637db9]
[Dock:298518] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x76327c82a1ca]
[Dock:298518] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x76327c82a28b]
[Dock:298518] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x5e13666390a5]
[Dock:298518] *** End of error message ***
*** buffer overflow detected ***: terminated
[Dock:298519] *** Process received signal ***
[Dock:298519] Signal: Aborted (6)
[Dock:298519] Signal code: (-6)
[Dock:298519] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x701e69845330]
[Dock:298519] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x701e6989eb2c]
[Dock:298519] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x701e6984527e]
[Dock:298519] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x701e698288ff]
[Dock:298519] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x701e698297b6]
[Dock:298519] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x701e69936c19]
[Dock:298519] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x701e699365d4]
[Dock:298519] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x701e699381b9]
[Dock:298519] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x5c18d2584eca]
[Dock:298519] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x5c18d2585f68]
[Dock:298519] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x5c18d2580db9]
[Dock:298519] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x701e6982a1ca]
[Dock:298519] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x701e6982a28b]
[Dock:298519] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x5c18d25820a5]
[Dock:298519] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 0 on node Dock exited on signal
6 (Aborted).
--------------------------------------------------------------------------
./Run.rism_selftest_kh: Program error
make[2]: [Makefile:341: test.rism3d.open] Error 1 (ignored)
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_selftest_pse3; fi
Running test to do basic MD (librism)
(trajectory processing using the 3D-RISM command line interface)
mpirun -np 4 /home/ibrahim/amber24///bin/rism3d.snglpnt.MPI
*** buffer overflow detected ***: terminated
*** buffer overflow detected ***: terminated
[Dock:298557] *** Process received signal ***
[Dock:298557] Signal: Aborted (6)
[Dock:298557] Signal code: (-6)
*** buffer overflow detected ***: terminated
[Dock:298558] *** Process received signal ***
[Dock:298558] Signal: Aborted (6)
[Dock:298558] Signal code: (-6)
*** buffer overflow detected ***: terminated
[Dock:298559] *** Process received signal ***
[Dock:298559] Signal: Aborted (6)
[Dock:298559] Signal code: (-6)
[Dock:298557] [ 0] [Dock:298558] [Dock:298559] [ 0]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x7b8aa2245330]
[Dock:298557] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x775d2b645330]
[Dock:298559] [ 1] [ 0]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x775d2b69eb2c]
[Dock:298559] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x7b8aa229eb2c]
[Dock:298557] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x775d2b64527e]
[Dock:298559] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x7b8aa224527e]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x734d61645330]
[Dock:298558] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x775d2b6288ff]
[Dock:298559] [ 4] [Dock:298557]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x734d6169eb2c]
[Dock:298558] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x775d2b6297b6]
[Dock:298559] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x734d6164527e]
[ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x775d2b736c19]
[Dock:298559] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7b8aa22288ff]
[Dock:298557] [ 4]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x775d2b7365d4]
[Dock:298558] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x7b8aa22297b6]
[Dock:298557] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x734d616288ff]
[Dock:298558] [ 4]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x7b8aa2336c19]
[Dock:298557] [ 6] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x734d616297b6]
[Dock:298558] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x7b8aa23365d4]
[Dock:298557] [ 7] [Dock:298559]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x734d61736c19]
[Dock:298558] [ 6] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x7b8aa23381b9]
[Dock:298557] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x6332ef1f0eca]
[Dock:298557] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x6332ef1f1f68]
[Dock:298557] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x6332ef1ecdb9]
[Dock:298557] [11]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x734d617365d4]
[Dock:298558] [ 7] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x7b8aa222a1ca]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x734d617381b9]
[Dock:298558] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x59ad0f107eca]
[Dock:298558] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x59ad0f108f68]
[Dock:298558] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x59ad0f103db9]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x775d2b7381b9]
[Dock:298559] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x5ab2c4a98eca]
[Dock:298559] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x5ab2c4a99f68]
[Dock:298558] [11] [Dock:298559] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x5ab2c4a94db9]
[Dock:298559] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x734d6162a1ca]
[Dock:298558] [12] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x775d2b62a1ca]
[Dock:298559] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x734d6162a28b]
[Dock:298558] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x59ad0f1050a5]
[Dock:298558] *** End of error message ***
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x775d2b62a28b]
[Dock:298559] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x5ab2c4a960a5]
[Dock:298559] *** End of error message ***
[Dock:298557] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7b8aa222a28b]
[Dock:298557] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x6332ef1ee0a5]
[Dock:298557] *** End of error message ***
[Dock:298556] *** Process received signal ***
[Dock:298556] Signal: Aborted (6)
[Dock:298556] Signal code: (-6)
[Dock:298556] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x713c8c845330]
[Dock:298556] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x713c8c89eb2c]
[Dock:298556] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x713c8c84527e]
[Dock:298556] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x713c8c8288ff]
[Dock:298556] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x297b6)[0x713c8c8297b6]
[Dock:298556] [ 5]
/lib/x86_64-linux-gnu/libc.so.6(+0x136c19)[0x713c8c936c19]
[Dock:298556] [ 6]
/lib/x86_64-linux-gnu/libc.so.6(+0x1365d4)[0x713c8c9365d4]
[Dock:298556] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(+0x1381b9)[0x713c8c9381b9]
[Dock:298556] [ 8]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x9eca)[0x5df206714eca]
[Dock:298556] [ 9]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0xaf68)[0x5df206715f68]
[Dock:298556] [10]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x5db9)[0x5df206710db9]
[Dock:298556] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x713c8c82a1ca]
[Dock:298556] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x713c8c82a28b]
[Dock:298556] [13]
/home/ibrahim/amber24///bin/rism3d.snglpnt.MPI(+0x70a5)[0x5df2067120a5]
[Dock:298556] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 0 on node Dock exited on signal
6 (Aborted).
--------------------------------------------------------------------------
./Run.rism_selftest_pse3: Program error
make[2]: [Makefile:342: test.rism3d.open] Error 1 (ignored)
if [ -n "testrism" ]; then cd rism3d/ala &&
./Run.rism_sp_ljfit_boxset_fast; fi
DO_PARALLEL set to mpirun -np 4
./Run.rism_sp_ljfit_boxset_fast: This test requires 1 or 2 processes
for meaningful comparison.
if [ -n "testrism" ]; then cd rism3d/ala &&
./Run.rism_sp_ljfit_bufferset_fast; fi
DO_PARALLEL set to mpirun -np 4
./Run.rism_sp_ljfit_bufferset_fast: This test requires 1 or 2 processes
for meaningful comparison.
if [ -n "testrism" ]; then cd rism3d/ala &&
./Run.rism_sp_ljset_bufferfit_fast; fi
DO_PARALLEL set to mpirun -np 4
./Run.rism_sp_ljset_bufferfit_fast: This test requires 1 or 2 processes
for meaningful comparison.
if [ -n "testrism" ]; then cd rism3d/ala &&
./Run.rism_sp_ljset_bufferset_fast; fi
DO_PARALLEL set to mpirun -np 4
./Run.rism_sp_ljset_bufferset_fast: This test requires 1 or 2 processes
for meaningful comparison.
if [ -n "testrism" ]; then cd rism3d/ala &&
./Run.rism_sp_ljtol_bufferfit_fast; fi
DO_PARALLEL set to mpirun -np 4
./Run.rism_sp_ljtol_bufferfit_fast: This test requires 1 or 2 processes
for meaningful comparison.
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_sp_nacl_fast; fi
Running test to do basic MD (librism)
(trajectory processing using the 3D-RISM command line interface)
mpirun -np 4 /home/ibrahim/amber24///bin/rism3d.snglpnt.MPI
diffing rism3d.snglpnt.nacl.fast.out.check.totChg with
rism3d.snglpnt.nacl.fast.out.totChg
PASSED
==============================================================
diffing rism3d.snglpnt.nacl.fast.out.check.rel with
rism3d.snglpnt.nacl.fast.out.rel
PASSED
==============================================================
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_sp_nacl_tree_fast; fi
Running test to do basic MD (librism)
(trajectory processing using the 3D-RISM command line interface)
mpirun -np 4 /home/ibrahim/amber24///bin/rism3d.snglpnt.MPI
diffing rism3d.snglpnt.nacl.tree.fast.out.check.totChg with
rism3d.snglpnt.nacl.tree.fast.out.totChg
PASSED
==============================================================
diffing rism3d.snglpnt.nacl.tree.fast.out.check.rel with
rism3d.snglpnt.nacl.tree.fast.out.rel
PASSED
==============================================================
if [ -n "testrism" ]; then cd rism3d/ala && ./Run.rism_sp_tree_fast; fi
Running test to do basic MD (librism)
(trajectory processing using the 3D-RISM command line interface
with tree summation)
mpirun -np 4 /home/ibrahim/amber24///bin/rism3d.snglpnt.MPI
diffing rism3d.snglpnt.tree.fast.out.check.totChg with
rism3d.snglpnt.tree.fast.out.totChg
PASSED
==============================================================
diffing rism3d.snglpnt.tree.fast.out.check.rel with
rism3d.snglpnt.tree.fast.out.rel
PASSED
==============================================================
if [ -n "testrism" ]; then cd rism3d/4lzta && ./Run.4lzta.kh.pme; fi
DO_PARALLEL set to mpirun -np 4; max is 2
if [ -n "testrism" ]; then cd rism3d/1ahoa && ./Run.1ahoa.kh.pme; fi
DO_PARALLEL set to mpirun -np 4; max is 2
if [ -n "testrism" ]; then cd rism3d/PH4+_triclinic &&
./Run.PH4+_triclinic.kh.pme.center0; fi
DO_PARALLEL set to mpirun -np 4; max is 2
if [ -n "testrism" ]; then cd rism3d/PH4+_triclinic &&
./Run.PH4+_triclinic.kh.pme.center1; fi
DO_PARALLEL set to mpirun -np 4; max is 2
if [ -n "testrism" ]; then cd rism3d/PH4+_triclinic &&
./Run.PH4+_triclinic.kh.pme.center2; fi
DO_PARALLEL set to mpirun -np 4; max is 2
cd bar_pbsa && ./Run.bar_pbsa
Running BAR/PBSA with 4 threads
Skipping complex runs with 4 threads
Namespace(command='strip', strip_input='1C5X_inputs/strip_input.yaml')
{'dest_path': '1C5X', 'complex_paths': ['./1C5X_explicit/t1/complex'],
'ligand_paths': ['./1C5X_explicit/t1/ligands'], 'ligand_mask': ':DRG',
'ion_decharge': True, 'last_half_frames': True, 'stride': 1}
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.000
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.200
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.400
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.600
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.800
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/1.000
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.000
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.200
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.400
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.600
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.800
mkdir /home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/1.000
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.000
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.200
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.400
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.600
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.800
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/1.000
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
./1C5X_explicit/t1/ligands, lambda: 0.000, mask: :DRG|.32
./1C5X_explicit/t1/ligands, lambda: 0.200, mask: :DRG|.32
./1C5X_explicit/t1/ligands, lambda: 0.400, mask: :DRG|.32
./1C5X_explicit/t1/ligands, lambda: 0.600, mask: :DRG|.32
./1C5X_explicit/t1/ligands, lambda: 0.800, mask: :DRG|.32
./1C5X_explicit/t1/ligands, lambda: 1.000, mask: :DRG|.32
./1C5X_explicit/t1/complex, lambda: 0.000, mask: :1-245|:DRG|.3862
./1C5X_explicit/t1/complex, lambda: 0.200, mask: :1-245|:DRG|.3862
./1C5X_explicit/t1/complex, lambda: 0.400, mask: :1-245|:DRG|.3862
./1C5X_explicit/t1/complex, lambda: 0.600, mask: :1-245|:DRG|.3862
./1C5X_explicit/t1/complex, lambda: 0.800, mask: :1-245|:DRG|.3862
./1C5X_explicit/t1/complex, lambda: 1.000, mask: :1-245|:DRG|.3862
align 1C5X ligands 0.000
align 1C5X ligands 0.200
align 1C5X ligands 0.400
align 1C5X ligands 0.600
align 1C5X ligands 0.800
align 1C5X ligands 1.000
align 1C5X complex 0.000
align 1C5X complex 0.200
align 1C5X complex 0.400
align 1C5X complex 0.600
align 1C5X complex 0.800
align 1C5X complex 1.000
Namespace(command='prep', prep_input='1C5X_inputs/prep_input.yaml')
{'dest_path': '1C5X', 'ligand_res': 'DRG', 'istrng': 150, 'epsin': 1.0,
'radiscale': 1.0, 'protscale': 1.0}
setup
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0
setup
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_complex/e_1.0_r_1.0_p_1.0
1C5X ligands
PB energy calculation
&cntrl
imin = 5, nstlim = 2, dt = 0.002,
ntx = 2, irest = 0,
ntb = 0,
ntt = 1,
temp0 = 298.0, ig = -1,
ntp = 0,
ntc = 2, ntf = 2,
ioutfm = 1, iwrap = 0,
ntwe = 1000, ntwx = 10000, ntpr = 1, ntwr = 10000,
cut = 9999.0,
maxcyc = 1,
ipb=2, inp=0
/
&pb
npbverb=0, istrng=150, epsout=80.0, epsin=1.0, space=.5,
accept=0.001, radiopt=0, fillratio=4,
npbopt=0, bcopt=1, solvopt=1, maxitn=10000,
frcopt=0, nfocus=2, radiscale=1.0, radires="DRG", protscale=1.0,
dprob=1.4
/
1C5X complex
PB energy calculation
&cntrl
imin = 5, nstlim = 2, dt = 0.002,
ntx = 2, irest = 0,
ntb = 0,
ntt = 1,
temp0 = 298.0, ig = -1,
ntp = 0,
ntc = 2, ntf = 2,
ioutfm = 1, iwrap = 0,
ntwe = 1000, ntwx = 10000, ntpr = 1, ntwr = 10000,
cut = 9999.0,
maxcyc = 1,
ipb=2, inp=0
/
&pb
npbverb=0, istrng=150, epsout=80.0, epsin=1.0, space=.5,
accept=0.001, radiopt=0, fillratio=2,
npbopt=0, bcopt=1, solvopt=1, maxitn=10000,
frcopt=0, nfocus=2, radiscale=1.0, radires="DRG", protscale=1.0,
dprob=1.4
/
Namespace(command='run', run_input='1C5X_inputs/ligands_run_input.yaml',
num_processes=4)
{'dest_path': '1C5X', 'epsin': 1.0, 'radiscale': 1.0, 'protscale': 1.0,
'ligcom': 'ligands', 'del_traj': True}
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.000.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.000.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.000_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.000_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.200.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.200.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.200_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.200_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.200.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.200.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.200_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.200_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.400.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.400.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.400_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.400_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.200/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.200.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.200.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.200_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.200_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.400.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.400.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.400_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.400_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.600.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.600.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.600_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.600_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.400/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.400.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.400.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.400_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.400_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.600.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.600.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.600_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.600_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.800.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.800.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.800_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.800_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.600/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.600.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.600.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.600_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.600_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.800.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.800.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.800_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.800_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/1.000/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_1.000.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_1.000.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_1.000_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_1.000_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/1.000/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/1.000/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_1.000.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/1.000/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_1.000.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_1.000_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_1.000_mden
/home/ibrahim/amber24///bin/sander -i
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
-c
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/1.000/ti.ncrst
-p
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.800/ti.parm
-O -o
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_0.800.out
-y
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/1.000/
ti001.nc -r
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_0.800.ncrst
-x
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_0.800_mdcrd
-e
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_0.800_mden
Namespace(command='calc', calc_input='1C5X_inputs/ligands_run_input.yaml')
{'dest_path': '1C5X', 'epsin': 1.0, 'radiscale': 1.0, 'protscale': 1.0,
'ligcom': 'ligands', 'del_traj': True}
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.200.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.000.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.200.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.400.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.200.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.400.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.600.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.400.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.600.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.800.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.600.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.800.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_1.000.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_0.800.out
parsing
/home/ibrahim/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_1.000.out
1C5X ligands
bar_total: 279.52937519976405
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
diffing 1C5X_save/concat_ligands/0.000/ti.parm with
1C5X/concat_ligands/0.000/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_ligands/0.200/ti.parm with
1C5X/concat_ligands/0.200/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_ligands/0.400/ti.parm with
1C5X/concat_ligands/0.400/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_ligands/0.600/ti.parm with
1C5X/concat_ligands/0.600/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_ligands/0.800/ti.parm with
1C5X/concat_ligands/0.800/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_ligands/1.000/ti.parm with
1C5X/concat_ligands/1.000/ti.parm
PASSED
==============================================================
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
diffing 1C5X_save/concat_complex/0.000/ti.parm with
1C5X/concat_complex/0.000/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_complex/0.200/ti.parm with
1C5X/concat_complex/0.200/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_complex/0.400/ti.parm with
1C5X/concat_complex/0.400/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_complex/0.600/ti.parm with
1C5X/concat_complex/0.600/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_complex/0.800/ti.parm with
1C5X/concat_complex/0.800/ti.parm
PASSED
==============================================================
diffing 1C5X_save/concat_complex/1.000/ti.parm with
1C5X/concat_complex/1.000/ti.parm
PASSED
==============================================================
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
Error: NcTest: 'ncdump' not found, required for NcTest.
diffing 1C5X_save/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt with
1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt
PASSED
==============================================================
diffing 1C5X_save/param_sweep_complex/e_1.0_r_1.0_p_1.0/pb_input.txt with
1C5X/param_sweep_complex/e_1.0_r_1.0_p_1.0/pb_input.txt
PASSED
==============================================================
diffing 1C5X_save/param_sweep_ligands/e_1.0_r_1.0_p_1.0/energies.csv with
1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/energies.csv
PASSED
==============================================================
diffing 1C5X_save/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_final.txt with
1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_final.txt
PASSED
==============================================================
MPI command: mpirun -np 4
Testing QUICK-24.03 mpi version started on 04/13/2025 at 07:58:35 PM.
Running test 1 of 25
PSB5: RHF energy test: s and p basis functions
diffing ene_psb5_rhf_631g.ref.ene with ene_psb5_rhf_631g.ene
PASSED
==============================================================
diffing ene_psb5_rhf_631g.ref.dipole with ene_psb5_rhf_631g.dipole
PASSED
==============================================================
Running test 2 of 25
Acetone: RHF energy test: s and p basis functions
diffing ene_acetone_rhf_321g.ref.ene with ene_acetone_rhf_321g.ene
PASSED
==============================================================
diffing ene_acetone_rhf_321g.ref.dipole with ene_acetone_rhf_321g.dipole
PASSED
==============================================================
Running test 3 of 25
PSB3: DFT energy test: s and p basis functions, BLYP functional
diffing ene_psb3_blyp_631g.ref.ene with ene_psb3_blyp_631g.ene
PASSED
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Received on Mon Apr 14 2025 - 03:30:02 PDT
