[gmx-users] Out of disk space

[Mark Abraham]

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.abraham at gmail.com>
wrote:

>
>
>
> On Tue, Jun 3, 2014 at 10:35 PM, Carlos Familia <carlosfamilia at 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 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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>>
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>
>