Re: [gmx-users] do_dssp crashes on certain machines..
hi, On Thursday, 19. April 2007 17:23, Mark Abraham wrote: > [EMAIL PROTECTED] wrote: > > Dear community, > > > > I have the following problem with do_dssp, when I try analysing a long 70 > > ns trajectory produced by a REMD calculation. All my previous analysis > > went fine, when the trajectory had a length of ~= 50ns. However, I now > > obtain the following errror message, perhaps one hour after launching > > do_dssp, when the standard error message says frames around 54ns are > > being analysed: > > > > > > Group12 ( Cl) has 8 elements > > Group13 ( SOL) has 42228 elements > > Group14 ( Other) has 42236 elements > > Select a group: There are 103 residues in your selected group > > Opening library file > > /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map > > Reading frame 0 time0.000 > > Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# > > Reading frame 36630 time 54945.000 > > --- > > Program do_dssp, VERSION 3.3 > > Source code file: futil.c, line: 340 > > > > File input/output error: > > ddr3C7fs > > --- > > > > > > I guess this problem is due to the architecture/memory of the nodes of > > the cluster I use (where this error occurs whether do_dssp is the only > > job on the node or not): The same analysis works fine on another machine. > > The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD > > Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus > > and 4*1GB memory. > > > > I thank you very much for any suggestions! > > Do the analysis piecewise... trjconv to break the .trr into chunks, and > now you can even do the analysis in parallel. Could be a nice application for pushing parallel filesystems to its limits! Perhaps it could be implemented in upcoming gromacs versions, something like mpich wrapper for certain analysis tools. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Grettings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp crashes on certain machines..
[EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Do the analysis piecewise... trjconv to break the .trr into chunks, and now you can even do the analysis in parallel. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] do_dssp crashes on certain machines..
Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Pascal Baillod *** Pascal Baillod (PhD student) *** Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322 Institute of Chemical Sciences and Engineering ,Fax: +41-(0)21-693-0320 Laboratory of Computational Chemistry and Biochemistry [EMAIL PROTECTED] Room BCH 4121, Avenue Forel,http://lcbcpc21.epfl.ch CH-1015 Lausanne *** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
