Re: [gmx-users] Out of disk space
Choosing appropriate output-frequency settings, nsteps to cap your file
size, and mdrun -noappend is likely your best approach.
Mark
On Wed, Jun 4, 2014 at 8:54 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Tue, Jun 3, 2014 at 10:35 PM, Carlos Familia carlosfami...@gmail.com
wrote:
Hello,
I was running the final equilibration step (NTP) and i received an error
saying that i was running out of disk space, the trajectory file writen
has
2GB, and every retry will generate a file with the same size. I have
looked
for file size limit, but there is no limitation that i can find on my
system. I am runing arch linux on a 32bits computer (i686),
That is likely a limitation that is manifest in whatever library stack is
supporting the file writing that GROMACS is using. If (say) the C library
uses a 32-bit integer for the size, bang you're dead.
the file system
is ext4, have 2GB of ram, and 64GB of disk available.
The command issued was:
mdrun -v -deffnm npt
The gromacs message was:
Program mdrun, VERSION 4.6.5
Source code file:
.../aur-gromacs-mpi/src/gromacs-4.6.5/src/gmxlib/trnio.c, line: 311
File input/output error:
Cannot write trajectory frame; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the
GROMACS
I have also runned the comman ulimit -a, that showed:
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 30
file size (blocks, -f) unlimited
pending signals (-i) 16117
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size(512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 99
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 16117
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
Additionally i run a program to write 2.5 GB to disk in c++, that
generated
the 2.5GB file without any problem:
#include iostream
#include fstream
#include vector
int main()
{
std::vectorchar empty(1024, 0);
std::ofstream ofs(ouput.img, std::ios::binary | std::ios::out);
for(int i = 0; i 1024*2560; i++)
{
if (!ofs.write(empty[0], empty.size()))
{
std::cerr problem writing to file std::endl;
return 255;
}
}
}
Any ideas on how to solve this?
Use a 64-bit operating system ;-) This is a problem users of your
operating system have likely encountered before, so if there is (say) a C
library that is compiled in some kind of 64-bit work-around mode, you may
be able to use that. The C++ library seems like it may have such a back end.
I know that i can change the parameters in the mdp file in order to
generate smaller files, but i was looking for a different solution that
wouldn't require this.
Is there any option to mdrun that could split the trajectory file for a
specified size?
No.
Mark
Thanks,
Carlos FamÃlia
--
Carlos Familia, MSc , PharmD
ISCSEM Pharmacology Assistant Lecturer
ISCSEM Laboratory of Molecular Pathology Researcher
Tel. +351 212946700 (Main) / +351 212946769 (Lab)
e-mail: carlosfami...@gmail.com / carlosfami...@egasmoniz.edu.pt
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Re: [gmx-users] Out of Disk Space
i had a same type of problem when i was using gromacs 4.6.4 version .. the problem was with 32 bit system..when i changed to 64 bit operating system evrything went on fine. but in my case i was getting same error (disk space error) after 2.2 gb file was generated although i had 800 gb free space. hope it will help . best - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/Out-of-Disk-Space-tp5014938p5015280.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Out of Disk Space
Hi Pavan, When you use the grompp command to prepare the md.tpr file for the final mdrun, do you notice such a statement This run will generate roughly X Mb of data. I suspect the resultant trajectory could be exceeding the available space. On Tue, Mar 4, 2014 at 4:12 PM, Pavan Kumar kumar.pavan...@gmail.comwrote: Hi everybody, I am running mdrun_mpi V 4.6.5 for nsteps=1000; 20 ns My simulation is getting stopped at 500ps and I am getting following error even though i have enough space on my cluster around 17 GB. *Cannot fsync 'md1.trr'; maybe you are out of disk space?* *Cannot fsync 'md1.log'; maybe you are out of disk space?* I have executed for two times, each time i get different error. What is the reason for the above error. I am sharing my mdp file. Any help is appreciated. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Out of Disk Space
It could be a quota issue (there is free space, but your group has used its entire allocation). Also, file systems often have limits not only on the total amount of space, but also on the total number of files that a group is allowed to create. Talk to your system administrator. There is likely a special command that you can run to find the relevant information (e.g., quota, diskUsage, prquota, etc... these are usually scripts written by your administrators so the name could in theory be anything). Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Pavan Kumar kumar.pavan...@gmail.com Sent: 04 March 2014 09:38 To: gmx-users Subject: Re: [gmx-users] Out of Disk Space Hello THOMMAS, Exactly, it showed 2.2GB of trajectory is going to be created. But i have 17GB of free space on my cluster on which i am running. So any other reasons for the error. Thanks in advance. On Tue, Mar 4, 2014 at 8:00 PM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Hi Pavan, When you use the grompp command to prepare the md.tpr file for the final mdrun, do you notice such a statement This run will generate roughly X Mb of data. I suspect the resultant trajectory could be exceeding the available space. On Tue, Mar 4, 2014 at 4:12 PM, Pavan Kumar kumar.pavan...@gmail.com wrote: Hi everybody, I am running mdrun_mpi V 4.6.5 for nsteps=1000; 20 ns My simulation is getting stopped at 500ps and I am getting following error even though i have enough space on my cluster around 17 GB. *Cannot fsync 'md1.trr'; maybe you are out of disk space?* *Cannot fsync 'md1.log'; maybe you are out of disk space?* I have executed for two times, each time i get different error. What is the reason for the above error. I am sharing my mdp file. Any help is appreciated. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Thanks Regards, Pavan Kumar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Out of Disk Space
I have executed for two times, each time i get different error. And you got *different* errors... What's the difference? Did you get the error at exactly the same integration time-step? Did you try to resproduce the error on another disk partition? Dr. Vitaly V. Chaban -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
On 12/4/13 5:24 AM, a...@imtech.res.in wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up someone's disk if it has several hundred GB available, but it can't hurt to reduce the output a bit. Frequent writing could be taxing the filesystem unnecessarily. It is also important to keep in mind that some desktop computers simply cannot handle a simulation that would be best run on a cluster with high-performance I/O. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
If none of the earlier suggestions worked then, it could be a simple problem of power port from which you have connected your hard disk. Try reconnecting the hard disk and and retry running the mdrun. Posting the exact commands used while writing the output during mdrun, may help to trace the problem. On Thu, Dec 5, 2013 at 11:03 AM, vaani vsha...@imtech.res.in wrote: On 12/4/13 5:24 AM, amin@.res wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up someone's disk if it has several hundred GB available, but it can't hurt to reduce the output a bit. Frequent writing could be taxing the filesystem unnecessarily. It is also important to keep in mind that some desktop computers simply cannot handle a simulation that would be best run on a cluster with high-performance I/O. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 hi justin, i have already run simulations on this work station before also without any such disk space problem. i am facing this problem now only after installing ubuntu and gromacs freshly, best - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013086.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- *Thanks and Regards,Bipin Singh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
hi chandan.. output for ls -1 is as follows: the directory from where i am running simulatons is in desktop .. and i have all the permissions for it. i am not that used to ubuntu and your suggestion will be of great help .. total 52 drwxrwxrwx 9 vansh vansh 4096 Nov 22 14:40 Desktop drwxr-xr-x 2 vansh vansh 4096 Nov 26 15:13 Documents drwxr-xr-x 8 vansh vansh 4096 Dec 3 16:43 Downloads -rw-r--r-- 1 vansh vansh 8445 Nov 12 10:03 examples.desktop -rw-rw-r-- 1 vansh vansh 5083 Dec 3 11:20 md.log drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Music drwxr-xr-x 2 vansh vansh 4096 Nov 13 22:49 Pictures drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Public drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Templates drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Videos - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013023.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
Dear vaani, Please rerun the gmx executable. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 11:20 AM, vaani vsha...@imtech.res.in wrote: hi chandan.. output for ls -1 is as follows: the directory from where i am running simulatons is in desktop .. and i have all the permissions for it. i am not that used to ubuntu and your suggestion will be of great help .. total 52 drwxrwxrwx 9 vansh vansh 4096 Nov 22 14:40 Desktop drwxr-xr-x 2 vansh vansh 4096 Nov 26 15:13 Documents drwxr-xr-x 8 vansh vansh 4096 Dec 3 16:43 Downloads -rw-r--r-- 1 vansh vansh 8445 Nov 12 10:03 examples.desktop -rw-rw-r-- 1 vansh vansh 5083 Dec 3 11:20 md.log drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Music drwxr-xr-x 2 vansh vansh 4096 Nov 13 22:49 Pictures drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Public drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Templates drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Videos - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013023.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
Dear vaani, Sorry for the unclear message. Try running the mdrun command once again and post the out put of the log file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 12:34 PM, vaani vsha...@imtech.res.in wrote: i am sorry ..but i kind of dint get you .. - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013027.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
sure .. - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013029.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] out of disk space error
vaani wrote nvt.log http://gromacs.5086.x6.nabble.com/file/n5013030/nvt.log find the attached nvt.log file .. i have been equilibrating for 200ps in this example..and getting this error , but when equilibrating for 100ps there is no such error ..in later case i am getting this error at the time of 10 ns dynamic run - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013032.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
