[gmx-users] Error DSSP Gromacs 5.0.4

Justin Lemkul jalemkul at vt.edu
Thu Nov 5 16:38:02 CET 2015 


On 11/5/15 10:36 AM, João Henriques wrote:
> Now I'm just curious, why would compiling do_dssp with MPI and/or double
> precision make work incorrectly? I understand why it is absolutely
> unnecessary, I just don't see why it can mess things up.
>

I don't know but I've seen compilers do strange things in years past.

> Also, running commands as root is probably the most likely cause.
>

Agreed.

-Justin

> /J
>
> On Thu, Nov 5, 2015 at 4:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/5/15 10:26 AM, Stefania Evoli wrote:
>>
>>> I did the following steps:
>>>
>>> Downloaded the executable from the dssp site (dssp-2.0.4-amd64 or
>>> dssp-2.0.4-i386)
>>> renamed the file to dssp
>>> chmod -R u=rwx dssp
>>> sudo mv dssp/usr/local/bin/
>>> export DSSP=/usr/local/bin/dssp
>>> Added export DSSP=/usr/local/bin/dssp into the bashrc ad sourced it
>>>
>>>
>> The problem does not come from the dssp binary.  The do_dssp program is
>> just a wrapper to call dssp; do_dssp is writing intermediate dd* files that
>> somehow have the wrong permission.  Your do_dssp binary (based on the name)
>> is compiled as double-precision, with MPI.  Neither is necessary.
>> Recompile without MPI to make sure it wasn't simply compiled wrong.
>>
>> Also make sure you're not trying to invoke the command via sudo, as root,
>> etc.
>>
>> -Justin
>>
>>
>>
>>>
>>>
>>> —Dr. Stefania Evoli
>>> Post-Doctoral Fellow
>>> King Abdullah University of Science and Technology
>>> Catalysis center - Bldg. 3, 4th floor, 4231–WS18
>>> Thuwal, Kingdom of Saudi Arabia
>>> stefania.evoli at kaust.edu.sa
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 11/5/15, 6:16 PM, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>>> on
>>> behalf of João Henriques"
>>> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
>>> joao.henriques.32353 at gmail.com> wrote:
>>>
>>> ​DSSP is writing dd* files with root read/write rights only.​ How did you
>>>> compile it? It's hard to solve the problem without actually sitting in
>>>> front of the computer and check things myself.
>>>>
>>>> /J
>>>>
>>>> On Thu, Nov 5, 2015 at 3:55 PM, Stefania Evoli
>>>> <stefania.evoli at kaust.edu.sa>
>>>> wrote:
>>>>
>>>> I tried everything discussed in the following link but the problem
>>>>> remains
>>>>> the same.
>>>>>
>>>>> [gmx-users] Problem executing do_dssp in gromacs (Aarti rana | 13 Feb
>>>>> 10:41 2015)
>>>>>
>>>>>
>>>>> I tried also ./dssp in the folder /usr/local/bin (where the executable
>>>>> is
>>>>> and the same of export DSSP) and it works.
>>>>>
>>>>> Please someone can help me? It could be a problem of version
>>>>> downloaded? I
>>>>> tried with both dssp-2.0.4-linux-amd64 and dssp-2.0.4-linux-i386 but
>>>>> when
>>>>> I ran the command do_dssp_mpi_d -f x.xtc -s x.tpr still I had the
>>>>> following error
>>>>>
>>>>> -------------------------------------------------------
>>>>> Program do_dssp_mpi_d, VERSION 5.0.4
>>>>> Source code file:
>>>>> /home/evolis/gromacs-5.0.4/src/gromacs/fileio/futil.cpp,
>>>>> line: 863
>>>>>
>>>>> Fatal error:
>>>>> Permission denied for opening dd4CAvLj
>>>>> For more information and tips for troubleshooting, please check the
>>>>> GROMACS
>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>> -------------------------------------------------------
>>>>>
>>>>>
>>>>> Thank you,
>>>>> Stefania
>>>>>
>>>>> —Dr. Stefania Evoli
>>>>> Post-Doctoral Fellow
>>>>> King Abdullah University of Science and Technology
>>>>> Catalysis center - Bldg. 3, 4th floor, 4231–WS18
>>>>> Thuwal, Kingdom of Saudi Arabia
>>>>> stefania.evoli at kaust.edu.sa
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 11/4/15, 4:29 PM, "Stefania Evoli" <stefania.evoli at kaust.edu.sa>
>>>>> wrote:
>>>>>
>>>>> I¹m in the directory Œtest¹ that allows me to write.
>>>>>>
>>>>>> evolis at kw12572:~/NMDA_Llactate$ ls -lht
>>>>>> total 8.5G
>>>>>> drwxrwxr-x 2 evolis evolis 4.0K Nov  4 16:13 test
>>>>>>
>>>>>> However, after typing the do_dssp_mpi_d command, the files that are
>>>>>> created by Gromacs are empty and I get the same fatal error
>>>>>>
>>>>>> evolis at kw12572:~/NMDA_Llactate/test$ ls -ltr
>>>>>> total 13476
>>>>>> -rw-rw-r-- 1 evolis evolis 8905116 Nov  4 16:12 0-50ns.xtc
>>>>>> -rw-rw-r-- 1 evolis evolis 3589080 Nov  4 16:13 md.tpr
>>>>>> -rw-rw-r-- 1 evolis evolis 1298388 Nov  4 16:13 index.ndx
>>>>>> -rw--w---- 1 evolis evolis       0 Nov  4 16:13 ddI8Uu7p
>>>>>> -rw------- 1 evolis evolis       0 Nov  4 16:15 ddRoi6XU
>>>>>> -rw------- 1 evolis evolis       0 Nov  4 16:22 ddkcilMK
>>>>>>
>>>>>> I tried to change umask to 0000 but it doesn¹t solve the problem. Any
>>>>>> ideas?
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>> Stefania
>>>>>>
>>>>>> ‹Dr. Stefania Evoli
>>>>>> Post-Doctoral Fellow
>>>>>> King Abdullah University of Science and Technology
>>>>>> Catalysis center - Bldg. 3, 4th floor, 4231­WS18
>>>>>> Thuwal, Kingdom of Saudi Arabia
>>>>>> stefania.evoli at kaust.edu.sa
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 11/4/15, 4:13 PM, "
>>>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>>>>>>
>>>>> on
>>>>>
>>>>>> behalf of João Henriques"
>>>>>> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
>>>>>> joao.henriques.32353 at gmail.com> wrote:
>>>>>>
>>>>>> Probably has nothing to do with dssp and/or gromacs. Sounds like you
>>>>>>>
>>>>>> just
>>>>>
>>>>>> don't have permission to read and/or operate on the file. Have you
>>>>>>> checked
>>>>>>> the permissions of your work directory and similar stuff?
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> /J
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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>>>>>>
>>>>>>
>>>>>
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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

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