<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt">It is better for you to run the simulation for more time to see whether you can reproduce this error. <br>If the problem persists, NFS may first be considered and you may test for writing the trajectory on local disk. If still so (shall be very rare), memory is likely to be in fault.<br><br>NFS is also better mounted with option: hard.<br><div> </div>Regards,<br>Yang Ye<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: zazeri <zazeri@yahoo.com.br><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Monday, July 16, 2007 4:52:46 AM<br>Subject: Re: Re: [gmx-users] Magic number error<br><br><div>Chris,<br><br>I was forgetting
to tell you some things...<br><br>1) the trajectory in which I'm evaluation is part from<br>a simulation that is running still;<br>2) the machine where the simulation is running belongs<br>to a cluster, whose "/home" is connected by NFS to the<br>master machine;<br>3) the md.log and nohup.out do not accuse any mistake;<br>4) the edr file (energy file) is ok, I've noticed it<br>because I've calculated the system volume and the file<br>supplied the values besides <br>the instant that the xtc file has generated the error.<br>Besides, the system volume is good, the system did not<br>explode! :D<br>5) I'm saving the trajectory every 8 ps;<br>6) all the analyses, creation of tpr file and<br>simulation were made in the same machine. (Simulation<br>goes on running)<br><br>Other considerations:<br><br>gmxcheck:<br>(gmxcheck -f system.md.xtc -c system.md.tpr -e<br>ener.edr -n index.ndx)<br><br>Checking file system.md.xtc<br>Reading frame 0
time 0.000<br># Atoms 23924<br>Precision 0.001 (nm)<br>Reading frame 110 time 880.000 <br>-------------------------------------------------------<br>Program gmxcheck, VERSION 3.3.1<br>Source code file: xtcio.c, line: 83<br><br>Fatal error:<br>Magic Number Error in XTC file (read 0, should be<br>1995)<br>-------------------------------------------------------<br><br>g_potential, g_order and "mdrun -rerun" also give the<br>same error.<br>(mpirun -np 2 mdrun_mpi.lam -s system.md.tpr -rerun<br>system.md.xtc -o rerun.trr -x rerun.xtc -e<br>ener_rerun.edr -g rerun.log -v)<br>(The tpr file was generated for 2 nodes, one job for<br>each processor. There're 2 processors in each<br>machine(node)).<br><br>I've also verified the atom number and it's ok, 23924.<br><br>Thank you for the attention!<br><br><br><br><br>--- Chris Neale <chris.neale@utoronto.ca> escreveu:<br>> Sounds like unrecoverable
data loss. Can you<br>> reproduce the problem with a new mdrun? If so,<br>> please post more data including the<br>> entire output from the program (e.g. g_potential)<br>> that gives problems (but let's stick to gmxcheck for<br>> now). Also the log file from the<br>> mdrun would be good. Also the exact commands (copy<br>> and paste please instead or re-write) that you used<br>> for the mdrun and for the <br>> gmxcheck/g_potential.<br>> <br>> Since you're going to be re-running mdrun anyway,<br>> keep the nstlog to a large number so that log file<br>> doesn't become huge.<br>> <br>> Other things to question: are you running analysis<br>> on the same computer that you ran mdrun on? same<br>> compilation? same precision?<br><br><br><br> <br>____________________________________________________________________________________<br>Novo Yahoo! Cadê? - Experimente uma nova busca.<br><a
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