[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

[Justin Lemkul]

On 4/26/14, 4:54 AM, Andrew Bostick wrote:
> Dear Mark
>
> I'm apologize.  You are right. I should give more indication and
> information you to help me.
>
> I used chmod -R 777 directory containing pdb and mdp files. Then I did MD
> simulation again:
>
> (pdb2gmx ...> editconf ........> em ...> npt eq ...> md)
>
> My problem is in md step (md.trr file).
>
> 1) After using ls -l:
>
> -rw-r--r-- 1 pdfco pdfco 137377  April 22 09:37 box.gro
> -rw-r--r-- 1 pdfco pdfco 137377  April 22 09:37 conf.gro
> -rw-r--r-- 1 pdfco pdfco 139904  April 22 09:44 em.edr
> -rw-r--r-- 1 pdfco pdfco 1814139 April 22 09:44 em.gro
> -rw-r--r-- 1 pdfco pdfco 353777  April 22 09:44 em.log
> -rwxrwxrwx 1 pdfco pdfco 958     April 9 2012 em.mdp
> -rw-r--r-- 1 pdfco pdfco 1673608 April 22 09:43 em.tpr
> -rw-r--r-- 1 pdfco pdfco 483876  April 22 09:44 em.trr
> -rwxrwxrwx 1 pdfco pdfco 171111  April 16 16:20 hgh.pdb
> -rwxrwxrwx 1 pdfco pdfco 960     April 9 2012 ions.mdp
> -rw-r--r-- 1 pdfco pdfco 1672380 April 22 09:38 ions.tpr
> -rw-r--r-- 1 pdfco pdfco 972688  April 24 05:56 md.cpt
> -rw-r--r-- 1 pdfco pdfco 2105052 April 24 06:06 md.edr
> -rw-r--r-- 1 pdfco pdfco 4723361 April 24 06:07 md.job
> -rw-r--r-- 1 pdfco pdfco 1498538 April 24 06:07 md.log
> -rwxrwxrwx 1 pdfco pdfco 2251    April 14 10:18 md.mdp
> -rw-r--r-- 1 pdfco pdfco 11314   April 22 18:10 mdout.mdp
> -rw-r--r-- 1 pdfco pdfco 972688  April 24 05:56 md_prev.cpt
> -rw-r--r-- 1 pdfco pdfco 1995920 April 22 18:11 md.tpr
> -rw-r--r-- 1 pdfco pdfco 2147483647 April 24 06:07 md.trr   **************
> -rw-r--r-- 1 pdfco pdfco 322065544  April 24 06:06 md.xtc
> -rw-r--r-- 1 pdfco pdfco 972048  April 22 17:10 npt.cpt
> -rw-r--r-- 1 pdfco pdfco 337488  April 22 17:10 npt.edr
> -rw-r--r-- 1 pdfco pdfco 2781651 April 22 17:10 npt.gro
> -rw-r--r-- 1 pdfco pdfco 356914  April 22 17:10 npt.job
> -rw-r--r-- 1 pdfco pdfco 369014  April 22 17:10 npt.log
> -rwxrwxrwx 1 pdfco pdfco 2317    April 14 09:40 npt.mdp
> -rw-r--r-- 1 pdfco pdfco 972048  April 22 17:10 npt_prev.cpt
> -rw-r--r-- 1 pdfco pdfco 1963760 April 22 14:25 npt.tpr
> -rw-r--r-- 1 pdfco pdfco 484783632  April 22 17:10 npt.trr
> -rw-r--r-- 1 pdfco pdfco 72710736   April 22 18:08 npt.xtc
> -rw-r--r-- 1 pdfco pdfco 971700  April 22 12:26 nvt.cpt
> -rw-r--r-- 1 pdfco pdfco 283252  April 22 12:26 nvt.edr
> -rw-r--r-- 1 pdfco pdfco 2781651 April 22 12:26 nvt.gro
> -rw-r--r-- 1 pdfco pdfco 356883  April 22 12:26 nvt.job
> -rw-r--r-- 1 pdfco pdfco 383651  April 22 12:26 nvt.log
> -rwxrwxrwx 1 pdfco pdfco 2095    April 14 09:40 nvt.mdp
> -rw-r--r-- 1 pdfco pdfco 971700  April 22 12:26 nvt_prev.cpt
> -rw-r--r-- 1 pdfco pdfco 1963760 April 22 09:45 nvt.tpr
> -rw-r--r-- 1 pdfco pdfco 484783632  April 22 12:26 nvt.trr
> -rw-r--r-- 1 pdfco pdfco 72725876   April 22 14:23 nvt.xtc
> -rw-r--r-- 1 pdfco pdfco 48075   April 22 09:37 posre.itp
> -rw-r--r-- 1 pdfco pdfco 21027   April 22 09:45 pot.xvg
> -rw-r--r-- 1 pdfco pdfco 13065   April 22 18:10 pres.xvg
> -rw-r--r-- 1 pdfco pdfco 1815967 April 22 09:38 sol.gro
> -rw-r--r-- 1 pdfco pdfco 1814139 April 22 09:42 sol_ions.gro
> -rw-r--r-- 1 pdfco pdfco 12963   April 22 14:24 temperature.xvg
> -rw-r--r-- 1 pdfco pdfco 12937   April 22 18:09 temp.xvg
> -rw-r--r-- 1 pdfco pdfco 902275  April 22 09:42 topol.top
>
> 2) After using gmxcheck -f md.trr -m doc.tex:
>
> Checking file md.trr
> Reading frame 0 time 0.000
> # Atoms 40313
> Reading frame 2000 time 12000.000
> WARNING: Incomplete frame: nr 2219 time 13314
> Item #frames Timestep (ps)
> Step 2219 6
> Time 2219 6
> Lambda 2219 6
> Coords 2219 6
> Velocities 2219 6
> Forces 0
> Box 2219 6
>
> 3) After loading npt.gro and md.trr by VMD, there is no problem.
>
> Unfortunately, again,  I encountered with:
>
> Program mdrun, VERSION 4.6.3
> Source code file: /build/buildd/gromacs-4.6.3/src/gmxlib/trnio.c, line: 311
>
> File input/output error:
> Cannot write trajectory frame; maybe you are out of disk space?
>
>
> 4) After using df -h
>
> Filesystem      Size  Used Avail Use% Mounted on
> /dev/sda3       220G   14G  196G   7% /
> none            4.0K     0  4.0K   0% /sys/fs/cgroup
> udev            3.0G  4.0K  3.0G   1% /dev
> tmpfs           607M  1.3M  606M   1% /run
> none            5.0M     0  5.0M   0% /run/lock
> none            3.0G  152K  3.0G   1% /run/shm
> none            100M   64K  100M   1% /run/user
> /dev/sda6       245G   61G  184G  25% /media/pdfco/my dear
> /dev/sda2       220G   85G  136G  39% /media/pdfco/Windows
> /dev/sda5       245G   43G  202G  18% /media/pdfco/nazif
>
> Please help me to solve this problem.
>

Your file system probably doesn't support files larger than 2GB; your .trr is 
exactly that size.  Reduce your output frequency or do your simulation in 
shorter increments of time.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================