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), 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? 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? 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.