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::vector<char> 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 > -- > 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.