<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
Hi,<br><br>I don't know if you know eneconv and trjcat, these programs can merge your output.<br>So you can still do all your analysis.<br><br>Berk<br><br>> Date: Wed, 29 Jul 2009 23:48:36 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] -append on jugene overwrites trr<br>> <br>> Dr. Leonid Yelash wrote:<br>> > Hello all together,<br>> > <br>> > in my compilation of Gromacs 4.0.5 on JUGENE (a Blue<br>> > Gene/P machine in Jülich), the -append option does not<br>> > work properly.<br>> <br>> Possibly that's intrinsic to the way I/O is handled on BlueGene. It <br>> should be simple to create a test program that tries to append to an <br>> existing file.<br>> <br>> Mark<br>> <br>> > When i restart a simulation from a checkpoint, the mdrun<br>> > recognizes the checkpoint and -append (one can see it in<br>> > md.log), but instead of appending to md.log, traj.trr, ener.edr,<br>> > it overwrites them. The file offsets in state.cpt (printed<br>> > by gmxdump -cp) are shown here:<br>> > <br>> >> number of output files = 3<br>> >> output filename = md.log<br>> >> file_offset_high = 0<br>> >> file_offset_low = 21265<br>> >> output filename = traj.trr<br>> >> file_offset_high = 0<br>> >> file_offset_low = 9021240<br>> >> output filename = ener.edr<br>> >> file_offset_high = 0<br>> >> file_offset_low = 5872<br>> > <br>> > The same distribution compiled for JUMP (a Power6 machine<br>> > running under AIX) works correctly. Details to the machines<br>> > can be found here<br>> > http://www.fz-juelich.de/jsc/service/sco_ibmBGP<br>> > http://www.fz-juelich.de/jsc/service/sco_ibmP6<br>> > <br>> > Does anybody know how to solve/work around? At the<br>> > moment i have to store continuations of a simulation run into<br>> > different directories, which complicates analysing data, e.g.<br>> > the calculation of time-dependent properties for the whole run.<br>> > <br>> > Many thanks in advance for any hints!<br>> > Leonid<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>