[gmx-developers] Fwd: Out of disk space

Carlos Familia carlosfamilia at gmail.com
Wed Jun 4 20:14:50 CEST 2014


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

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?


Carlos Família

Carlos Familia, MSc , PharmD
ISCSEM Pharmacology Assistant Lecturer
ISCSEM Laboratory of Molecular Pathology Researcher
Tel. +351 212946700 (Main) / +351 212946769 (Lab)
e-mail: carlosfamilia at gmail.com / carlosfamilia at egasmoniz.edu.pt
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