[gmx-users] question about mdrun -append
Berk Hess
gmx3 at hotmail.com
Fri Aug 7 16:11:48 CEST 2009
Strange...
I tested this combining procedure for other parts of the codes and there it works.
What kind of operating system are you running and what is the file system?
Berk
Date: Fri, 7 Aug 2009 14:49:45 +0200
From: qiaobf at gmail.com
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] question about mdrun -append
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: qiaobf at gmail.com
To: gmx-users at 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: qiaobf at gmail.com
To: gmx-users at 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
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