<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>We should remove the opening of the trr file in Gromacs 4.1 when no output is requested.<br>But opening one output file on one process should not cause a lot of system activity,<br>independently of the size of the cluster, right?<br><br>More costly are the fexist operations that all processes perform for all in and output files<br>with multiple possible file names. In git master only the master process calls fexist.<br><br>Berk <br><br>> Date: Wed, 2 Dec 2009 09:17:00 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] any chance to write avoid writing out trr but only xtc file ?<br>> <br>> We have the same desire on a large cluster in order to reduce the <br>> number of file operations overall. In addition to Xavier's suggestion, <br>> you can also write your .trr to memory:<br>> mdrun -deffnm xx -t /dev/shm/xx.trr<br>> or to the local disk:<br>> mdrun -deffnm xx -t ${TMPDIR}/xx.trr<br>> if those exist and depending on your architecture. Contact your <br>> sysadmin for the best option here... just be sure to rm -f your <br>> unwanted .trr.<br>> <br>> While I agree that the ability to not create the .trr at all or to <br>> write the .trr to /dev/null would be ideal, that appears to be <br>> incompatible with the automated file name extension determination and <br>> the provided solution will probably be just as fast.<br>> <br>> Chris.<br>> <br>> -- original message --<br>> <br>> you can define the frequency of writing to the trr file in the mdp file.<br>> <br>> using:<br>> <br>> nstxout = 0<br>> nstvout = 0<br>> nstfout =0<br>> <br>> should fix your problem.<br>> <br>> On Dec 1, 2009, at 4:30 PM, Jörn-Benjamin Lenz wrote:<br>> <br>> > dear users of gromacs,<br>> ><br>> > i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the <br>> > following problem:<br>> ><br>> > using the older version of gromacs I submitted REMD jobs to our <br>> > cluster (which also was updated from suse 10.3 to suse 11.1) and two <br>> > differently formatted output files were generated: trr files and <br>> > xtc files<br>> > since we always are short on disk space in our home folders i did <br>> > the following:<br>> > the trr files were written to the a folder in my home directory on <br>> > our fileserver whereas the xtc files were written to the local <br>> > machine i was using. in order to save disk storage on our fileserver <br>> > (i.e. in /home/joern/...) i deleted the trr files once as soon as <br>> > they were produced and the job on our cluster was still happy and <br>> > wrote the xtc files to my local machine and i was very happy with <br>> > that behaviour.<br>> ><br>> > using gromacs 4.0.5, again trr and xtc files are written. however, <br>> > as soon as i delete the trr files the mdrun jobs die and the whole <br>> > job finishes without keep on writing the xtc files as it did with <br>> > the older version.<br>> ><br>> > is there a chance to say gromacs not to write out a trr file at all <br>> > but only a xtc file. without using the mdrun -o command gromacs <br>> > still writes out the standard trajX.trr files. or is this becuase of <br>> > the update from suse 10.3 to suse 11.1 ?<br>> ><br>> > any help and / or advice is much appreciated !<br>> > many thanks in advance,<br>> ><br>> > joern<br>> > --<br>> <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 />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
</html>