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Hi Berk, The error still exist! The following process is used: 1. revise checkpoint.c under the source folder "~/programes/backups/gromacs-4.0.5/src/gmxlib" 2. make -j 4 3. cd ../../ (i. e., ~/programes/backups/gromacs-4.0.5) "make install mdrun" One of the output lines " /usr/bin/install -c -m 644 './ngmx.1' '/data1/HLRS/dgrid/stbw0172/programes/gromacs-4.0.5/bin//share/man/man1/ngmx.1'" says that the latest mdrun is installed in the right folder. Is there something wrong in the above process? or some further suggestions? thanks a lot! regards, Baofu Qiao Berk Hess wrote: I think this might be a bug in the checkpointing code. The negative number is correct, these are the lower 32 bits of the file offset. But they are combined incorrectly with the higher part.Could you try changing line 781 of src/gmxlib/checkpoint.c from: outputfiles[i].offset = ( ((off_t) offset_high) << 32 ) | ( (off_t) offset_low ); to outputfiles[i].offset = ( ((off_t) offset_high) << 32 ) | ( (off_t) offset_low & 4294967295U ); recompile gmxlib and mdrun and try to continue from the point that gave the error? You might want to copy all the files to make sure you do not loose anything. Please report back if this worked or not. Berk Date: Fri, 7 Aug 2009 12:10:04 +0200 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: Re: [gmx-users] question about mdrun -append Hi Berk, Thanks for your reply! The result of "gmxdump -cp T298.cpt" is given as follows (the long list of x, v, E is not shown) ************************************** number of output files = 4 output filename = T298.log file_offset_high = 0 file_offset_low = 7228659 output filename = T298.trr file_offset_high = 0 file_offset_low = 0 output filename = T298.xtc file_offset_high = 0 file_offset_low = -2020699160 output filename = T298.edr file_offset_high = 0 file_offset_low = 13270732 ************************************** But I don't know what this number means! On the other hand, another system, which can be continued using "mdrun -cpi T298.cpt", gives the following result of "gmxdump -cp T298.cpt" *************************************** number of output files = 4 output filename = T298.log file_offset_high = 0 file_offset_low = 7066641 output filename = T298.trr file_offset_high = 0 file_offset_low = 0 output filename = T298.xtc file_offset_high = 0 file_offset_low = 2144960064 output filename = T298.edr file_offset_high = 0 file_offset_low = 19540796 *************************************** It seems that the difference is: there is a negative number (-2020699160) in the former case. So what should I do? regards, Berk Hess wrote: My guess would be that for some reason (which I don't know), your xtc file has not been written to disk completely. You can check this by using gmxdump -cp on your checkpoint file and looking at the size of the xtc file. Berk Date: Fri, 7 Aug 2009 10:19:35 +0200 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about mdrun -append Hi all, I meet one problem when I am using mdrun -append. In some cases, the following error information happens, and mdrun is halted ************************************************* Program mdrun, VERSION 4.0.5 Source code file: checkpoint.c, line: 1248 Fatal error: Truncation of file T298.xtc failed. ************************************************* Line 1248 in checkpoint.c is the inner loop as follows ********************************************************************************* if(bAppendOutputFiles) { for(i=0;i<nfiles;i++) { if(0 != truncate(outputfiles[i].filename,outputfiles[i].offset) ) { gmx_fatal(FARGS,"Truncation of file %s failed.",outputfiles[i].filename); } } } ********************************************************************************* But I don't know how to solve it. Please give some suggestions! Thanks a lot! The following script is used grompp -f T298.mdp -c pre2.gro -p system.top -o T298 mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5 mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5 -cpi T298.cpt -append regards, Baofu Qiao _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _________________________________________________________________ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
