[gmx-users] orca and Segmentation fault
dear sir : I installed gromacs-orca for qm/mm ./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi make make install MPI is lam-mpi when run mdrun , the error Back Off! I just backed up md.log to ./#md.log.12# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! there we go! there we go! there we go! there we go! there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... [localhost:17937] *** Process received signal *** [localhost:17939] *** Process received signal *** [localhost:17937] Signal: Segmentation fault (11) [localhost:17937] Signal code: Address not mapped (1) [localhost:17937] Failing at address: 0x10 [localhost:17940] *** Process received signal *** [localhost:17939] Signal: Segmentation fault (11) [localhost:17939] Signal code: Address not mapped (1) [localhost:17939] Failing at address: 0x10 [localhost:17936] *** Process received signal *** [localhost:17936] Signal: Segmentation fault (11) [localhost:17936] Signal code: Address not mapped (1) [localhost:17936] Failing at address: 0x10 [localhost:17934] *** Process received signal *** [localhost:17938] *** Process received signal *** [localhost:17934] Signal: Segmentation fault (11) [localhost:17934] Signal code: Address not mapped (1) [localhost:17934] Failing at address: 0x10 [localhost:17940] Signal: Segmentation fault (11) [localhost:17940] Signal code: Address not mapped (1) [localhost:17940] Failing at address: 0x10 [localhost:17938] Signal: Segmentation fault (11) [localhost:17938] Signal code: Address not mapped (1) [localhost:17938] Failing at address: 0x10 [localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17939] [ 1] mdrun_dd [0x534a93] [localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17939] [ 6] mdrun_dd [0x41bcfa] [localhost:17939] *** End of error message *** [localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17936] [ 1] mdrun_dd [0x534a93] [localhost:17936] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17936] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17936] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17936] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17936] [ 6] mdrun_dd [0x41bcfa] [localhost:17936] *** End of error message *** [localhost:17940] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17940] [ 1] mdrun_dd [0x534a93] [localhost:17940] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17940] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17940] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17940] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17940] [ 6] mdrun_dd [0x41bcfa] [localhost:17940] *** End of error message *** there we go! [localhost:17935] *** Process received signal *** [localhost:17935] Signal: Segmentation fault (11) [localhost:17935] Signal code: Address not mapped (1) [localhost:17935] Failing at address: 0x10 [localhost:17935] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17935] [ 1] mdrun_dd [0x534a93] [localhost:17935] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17935] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17935] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17935] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17935] [ 6] mdrun_dd [0x41bcfa] [localhost:17935] *** End of error message *** [localhost:17934] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17934] [ 1] mdrun_dd [0x534a93] [localhost:17934] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17934] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17934] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17934] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17934] [ 6] mdrun_dd [0x41bcfa] [localhost:17934] *** End of error message *** [localhost:17937] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17937] [ 1] mdrun_dd [0x534a93] [localhost:17937] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17937] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17937] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17937] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17937] [ 6] mdrun_dd [0x41bcfa] [localhost:17937] *** End of error message *** [localhost:17938] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17938] [ 1] mdrun_dd [0x534a93] [localhost:17938] [ 2]
Re: [gmx-users] orca and Segmentation fault
Dear xi zhao, In your case GMX is applying threading and thus not only a single QM job is requested, but eight. You should run mdrun with -nt 1. Then GMX uses only one single CPU and ORCA is called only once (but can be used in parallel). Hope that helps, Christoph On 11/14/2011 10:34 AM, xi zhao wrote: dear sir : I installed gromacs-orca for qm/mm ./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi make make install MPI is lam-mpi when run mdrun , the error Back Off! I just backed up md.log to ./#md.log.12# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! there we go! there we go! there we go! there we go! there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... [localhost:17937] *** Process received signal *** [localhost:17939] *** Process received signal *** [localhost:17937] Signal: Segmentation fault (11) [localhost:17937] Signal code: Address not mapped (1) [localhost:17937] Failing at address: 0x10 [localhost:17940] *** Process received signal *** [localhost:17939] Signal: Segmentation fault (11) [localhost:17939] Signal code: Address not mapped (1) [localhost:17939] Failing at address: 0x10 [localhost:17936] *** Process received signal *** [localhost:17936] Signal: Segmentation fault (11) [localhost:17936] Signal code: Address not mapped (1) [localhost:17936] Failing at address: 0x10 [localhost:17934] *** Process received signal *** [localhost:17938] *** Process received signal *** [localhost:17934] Signal: Segmentation fault (11) [localhost:17934] Signal code: Address not mapped (1) [localhost:17934] Failing at address: 0x10 [localhost:17940] Signal: Segmentation fault (11) [localhost:17940] Signal code: Address not mapped (1) [localhost:17940] Failing at address: 0x10 [localhost:17938] Signal: Segmentation fault (11) [localhost:17938] Signal code: Address not mapped (1) [localhost:17938] Failing at address: 0x10 [localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17939] [ 1] mdrun_dd [0x534a93] [localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17939] [ 6] mdrun_dd [0x41bcfa] [localhost:17939] *** End of error message *** [localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17936] [ 1] mdrun_dd [0x534a93] [localhost:17936] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17936] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17936] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17936] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17936] [ 6] mdrun_dd [0x41bcfa] [localhost:17936] *** End of error message *** [localhost:17940] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17940] [ 1] mdrun_dd [0x534a93] [localhost:17940] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17940] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17940] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17940] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17940] [ 6] mdrun_dd [0x41bcfa] [localhost:17940] *** End of error message *** there we go! [localhost:17935] *** Process received signal *** [localhost:17935] Signal: Segmentation fault (11) [localhost:17935] Signal code: Address not mapped (1) [localhost:17935] Failing at address: 0x10 [localhost:17935] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17935] [ 1] mdrun_dd [0x534a93] [localhost:17935] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17935] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17935] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17935] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17935] [ 6] mdrun_dd [0x41bcfa] [localhost:17935] *** End of error message *** [localhost:17934] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17934] [ 1] mdrun_dd [0x534a93] [localhost:17934] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17934] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17934] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17934] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17934] [ 6] mdrun_dd [0x41bcfa] [localhost:17934] *** End of error message *** [localhost:17937] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17937] [ 1] mdrun_dd [0x534a93] [localhost:17937] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17937] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17937] [ 4] mdrun_dd(main+0xe69)
Re: [gmx-users] orca and Segmentation fault
./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi make make install I installed gromacs with Parallel mode, is not threading. when I run mpirun -np 1 mdrun_dd -v -s pyp.tpr or mdrun_dd -nt 1 -v -s pyp.tpr it still Back Off! I just backed up md.log to ./#md.log.20# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... Back Off! I just backed up traj.trr to ./#traj.trr.1# Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps, 0.5 ps. Calling 'orca pyp.inp pyp.out' Error : multiplicity (Mult:=2*S+1) is zero --- Program mdrun_dd, VERSION 4.5.1 Source code file: qm_orca.c, line: 393 Fatal error: Call to 'orca pyp.inp pyp.out' failed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The Carpenter Goes Bang Bang (The Breeders) Halting program mdrun_dd gcq#129: The Carpenter Goes Bang Bang (The Breeders) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 0 with PID 18080 on node localhost.localdomai exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). --- 11年11月14日，周一, Christoph Riplinger c...@thch.uni-bonn.de 写道： 发件人: Christoph Riplinger c...@thch.uni-bonn.de 主题: Re: [gmx-users] orca and Segmentation fault 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2011年11月14日,周一,下午6:51 Dear xi zhao, In your case GMX is applying threading and thus not only a single QM job is requested, but eight. You should run mdrun with -nt 1. Then GMX uses only one single CPU and ORCA is called only once (but can be used in parallel). Hope that helps, Christoph On 11/14/2011 10:34 AM, xi zhao wrote: dear sir : I installed gromacs-orca for qm/mm ./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi make make install MPI is lam-mpi when run mdrun , the error Back Off! I just backed up md.log to ./#md.log.12# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! there we go! there we go! there we go! there we go! there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... [localhost:17937] *** Process received signal *** [localhost:17939] *** Process received signal *** [localhost:17937] Signal: Segmentation fault (11) [localhost:17937] Signal code: Address not mapped (1) [localhost:17937] Failing at address: 0x10 [localhost:17940] *** Process received signal *** [localhost:17939] Signal: Segmentation fault (11) [localhost:17939] Signal code: Address not mapped (1) [localhost:17939] Failing at address: 0x10 [localhost:17936] *** Process received signal *** [localhost:17936] Signal: Segmentation fault (11) [localhost:17936] Signal code: Address not mapped (1) [localhost:17936] Failing at address: 0x10 [localhost:17934] *** Process received signal *** [localhost:17938] *** Process received signal *** [localhost:17934] Signal: Segmentation fault (11) [localhost:17934] Signal code: Address not mapped (1) [localhost:17934] Failing at address: 0x10 [localhost:17940] Signal: Segmentation fault (11) [localhost:17940] Signal code: Address not mapped (1) [localhost:17940] Failing at address: 0x10 [localhost:17938] Signal: Segmentation fault (11) [localhost:17938] Signal code: Address not mapped (1) [localhost:17938] Failing at address: 0x10 [localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17939] [ 1] mdrun_dd [0x534a93] [localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17939] [ 6] mdrun_dd [0x41bcfa] [localhost:17939] *** End of error message *** [localhost:17936] [ 0] /lib64/tls/libpthread.so.0
