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::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.