<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><A class=plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A><BR></DIV>
<DIV>./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi </DIV>
<DIV>make </DIV>
<DIV>make install </DIV>
<DIV>I installed gromacs with <SPAN id=result_box lang=en class=short_text closure_uid_bcy4dp="150" Tc="null" a="undefined" c="4"><SPAN class=hps closure_uid_bcy4dp="137" Tc="null">Parallel</SPAN></SPAN> 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</DIV>
<DIV>it still"</DIV>
<DIV>Back Off! I just backed up md.log to ./#md.log.20#<BR>Getting Loaded...<BR>Reading file pyp.tpr, VERSION 4.5.1 (single precision)<BR>Loaded with Money</DIV>
<DIV>QM/MM calculation requested.<BR>there we go!<BR>Layer 0<BR>nr of QM atoms 22<BR>QMlevel: B3LYP/3-21G</DIV>
<DIV>orca initialised...</DIV>
<DIV>Back Off! I just backed up traj.trr to ./#traj.trr.1#</DIV>
<DIV>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#</DIV>
<DIV>Back Off! I just backed up ener.edr to ./#ener.edr.2#<BR>starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'<BR>500 steps, 0.5 ps.<BR>Calling 'orca pyp.inp >> pyp.out'<BR>Error : multiplicity (Mult:=2*S+1) is zero</DIV>
<DIV>-------------------------------------------------------<BR>Program mdrun_dd, VERSION 4.5.1<BR>Source code file: qm_orca.c, line: 393</DIV>
<DIV>Fatal error:<BR>Call to 'orca pyp.inp >> pyp.out' failed</DIV>
<DIV>For more information and tips for troubleshooting, please check the GROMACS<BR>website at <A href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</A><BR>-------------------------------------------------------</DIV>
<DIV>"The Carpenter Goes Bang Bang" (The Breeders)</DIV>
<DIV>Halting program mdrun_dd</DIV>
<DIV>gcq#129: "The Carpenter Goes Bang Bang" (The Breeders)</DIV>
<DIV>--------------------------------------------------------------------------<BR>MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD <BR>with errorcode -1.</DIV>
<DIV>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<BR>You may or may not see output from other processes, depending on<BR>exactly when Open MPI kills them.<BR>--------------------------------------------------------------------------<BR>--------------------------------------------------------------------------<BR>mpirun has exited due to process rank 0 with PID 18080 on<BR>node localhost.localdomai exiting without calling "finalize". This may<BR>have caused other processes in the application to be<BR>terminated by signals sent by mpirun (as reported here)."</DIV>
<DIV><BR><BR>--- <B>11年11月14日，周一, Christoph Riplinger <I><cri@thch.uni-bonn.de></I></B> 写道：<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>发件人: Christoph Riplinger <cri@thch.uni-bonn.de><BR>主题: Re: [gmx-users] orca and Segmentation fault<BR>收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>日期: 2011年11月14日,周一,下午6:51<BR><BR>
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<DIV>Dear xi zhao,<BR><BR>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).<BR>Hope that helps,<BR>Christoph<BR><BR>On 11/14/2011 10:34 AM, xi zhao wrote:
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<DIV>dear sir : </DIV>
<DIV> I installed gromacs-orca for qm/mm</DIV>
<DIV>./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi </DIV>
<DIV>make </DIV>
<DIV>make install </DIV>
<DIV>MPI is lam-mpi</DIV>
<DIV> </DIV>
<DIV>when run mdrun , the error </DIV>
<DIV>" Back Off! I just backed up md.log to ./#md.log.12#<BR>Getting Loaded...<BR>Reading file pyp.tpr, VERSION 4.5.1 (single precision)<BR>Loaded with Money</DIV>
<DIV>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>QM/MM calculation requested.<BR>there we go!<BR>there we go!<BR>there we go!<BR>there we go!<BR>there we go!<BR>there we go!<BR>there we go!<BR>Layer 0<BR>nr of QM atoms 22<BR>QMlevel: B3LYP/3-21G</DIV>
<DIV>orca initialised...<BR>[localhost:17937] *** Process received signal ***<BR>[localhost:17939] *** Process received signal ***<BR>[localhost:17937] Signal: Segmentation fault (11)<BR>[localhost:17937] Signal code: Address not mapped (1)<BR>[localhost:17937] Failing at address: 0x10<BR>[localhost:17940] *** Process received signal ***<BR>[localhost:17939] Signal: Segmentation fault (11)<BR>[localhost:17939] Signal code: Address not mapped (1)<BR>[localhost:17939] Failing at address: 0x10<BR>[localhost:17936] *** Process received signal ***<BR>[localhost:17936] Signal: Segmentation fault (11)<BR>[localhost:17936] Signal code: Address not mapped (1)<BR>[localhost:17936] Failing at address: 0x10<BR>[localhost:17934] *** Process received signal ***<BR>[localhost:17938] *** Process received signal ***<BR>[localhost:17934] Signal: Segmentation fault (11)<BR>[localhost:17934] Signal code: Address not mapped (1)<BR>[localhost:17934] Failing at address:
0x10<BR>[localhost:17940] Signal: Segmentation fault (11)<BR>[localhost:17940] Signal code: Address not mapped (1)<BR>[localhost:17940] Failing at address: 0x10<BR>[localhost:17938] Signal: Segmentation fault (11)<BR>[localhost:17938] Signal code: Address not mapped (1)<BR>[localhost:17938] Failing at address: 0x10<BR>[localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]<BR>[localhost:17939] [ 1] mdrun_dd [0x534a93]<BR>[localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]<BR>[localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]<BR>[localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619]<BR>[localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb]<BR>[localhost:17939] [ 6] mdrun_dd [0x41bcfa]<BR>[localhost:17939] *** End of error message ***<BR>[localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]<BR>[localhost:17936] [ 1] mdrun_dd [0x534a93]<BR>[localhost:17936] [ 2]
mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]<BR>[localhost:17936] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]<BR>[localhost:17936] [ 4] mdrun_dd(main+0xe69) [0x43d619]<BR>[localhost:17936] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb]<BR>[localhost:17936] [ 6] mdrun_dd [0x41bcfa]<BR>[localhost:17936] *** End of error message ***<BR>[localhost:17940] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]<BR>[localhost:17940] [ 1] mdrun_dd [0x534a93]<BR>[localhost:17940] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]<BR>[localhost:17940] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]<BR>[localhost:17940] [ 4] mdrun_dd(main+0xe69) [0x43d619]<BR>[localhost:17940] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb]<BR>[localhost:17940] [ 6] mdrun_dd [0x41bcfa]<BR>[localhost:17940] *** End of error message ***<BR>there we go!<BR>[localhost:17935] *** Process received signal ***<BR>[localhost:17935] Signal: Segmentation fault
(11)<BR>[localhost:17935] Signal code: Address not mapped (1)<BR>[localhost:17935] Failing at address: 0x10<BR>[localhost:17935] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]<BR>[localhost:17935] [ 1] mdrun_dd [0x534a93]<BR>[localhost:17935] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]<BR>[localhost:17935] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]<BR>[localhost:17935] [ 4] mdrun_dd(main+0xe69) [0x43d619]<BR>[localhost:17935] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb]<BR>[localhost:17935] [ 6] mdrun_dd [0x41bcfa]<BR>[localhost:17935] *** End of error message ***<BR>[localhost:17934] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]<BR>[localhost:17934] [ 1] mdrun_dd [0x534a93]<BR>[localhost:17934] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]<BR>[localhost:17934] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]<BR>[localhost:17934] [ 4] mdrun_dd(main+0xe69) [0x43d619]<BR>[localhost:17934] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb)
[0x35c4f1c3fb]<BR>[localhost:17934] [ 6] mdrun_dd [0x41bcfa]<BR>[localhost:17934] *** End of error message ***<BR>[localhost:17937] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]<BR>[localhost:17937] [ 1] mdrun_dd [0x534a93]<BR>[localhost:17937] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]<BR>[localhost:17937] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]<BR>[localhost:17937] [ 4] mdrun_dd(main+0xe69) [0x43d619]<BR>[localhost:17937] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb]<BR>[localhost:17937] [ 6] mdrun_dd [0x41bcfa]<BR>[localhost:17937] *** End of error message ***<BR>[localhost:17938] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]<BR>[localhost:17938] [ 1] mdrun_dd [0x534a93]<BR>[localhost:17938] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]<BR>[localhost:17938] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]<BR>[localhost:17938] [ 4] mdrun_dd(main+0xe69) [0x43d619]<BR>[localhost:17938] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb)
[0x35c4f1c3fb]<BR>[localhost:17938] [ 6] mdrun_dd [0x41bcfa]<BR>[localhost:17938] *** End of error message ***<BR>Making 2D domain decomposition 4 x 2 x 1<BR>--------------------------------------------------------------------------<BR>mpirun noticed that process rank 3 with PID 17936 on node localhost.localdomai exited on signal 11 (Segmentation fault).<BR><BR><BR><A class=yiv353024604plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=yiv353024604pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A></DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE><BR></DIV></DIV><BR>-----下面为附件内容-----<BR><BR>
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