[gmx-users] Double precision test failure

[Chris Snook]

The gromacs commands are in my search path as both the commands 
suggested worked. The single precision tests worked but it was the 
double precision tests that completely failed.

All of the grompp.out files contain the single line error :

sh: line 1: grompp_d: command not found

Checking the bin directory, indeed there is no grompp_d binary. Was the 
Mac OS X binaries only compiled for single precision?

Chris

David van der Spoel wrote:
> Chris Snook wrote:
>> Yes,
>>
>> The paths for GMXBIN, GMXLDLIB, GMXDATA and GMXMAN are correctly 
>> defined whether
>> I use sh or bash as the shell. I do get the following errors when I 
>> run GMXRC in
>> either shell:
>>
>> ../bin/GMXRC: line 35: return: can only `return' from a function or 
>> sourced
>> script
>> ../bin/GMXRC: line 44: CSH:: command not found
>> ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error 
>> near
>> unexpected token `setenv'
>> ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (!
>> $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""'
>>
> you should in sh or bash type
>  . GMXRC
>
> the important question is whether the gromacs commands are in your 
> search path. this is best test by typing
> grompp -h
> or
> luck
>
> If they are there then something else is wrong in the test set. Please 
> check the grompp.out files in the subdirectories.
>
>> Regards
>>
>> Chris
>>
>> Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>>
>>> Chris Snook wrote:
>>>> I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 
>>>> 2.16GHz Core 2
>>>> Duo processor.
>>>>
>>>> I have downloaded and installed the v 3.3.2 binaries of gromacs for 
>>>> this OS and
>>>> run the test program. The single precision tests run OK. But the 
>>>> double
>>>> precision tests completely fail with the following output (partial):
>>>>
>>>> No topol.tpr file in angles1. grompp failed
>>>> FAILED. Check files in angles1
>>>> No topol.tpr file in angles125. grompp failed
>>>> FAILED. Check files in angles125
>>>> No topol.tpr file in bham. grompp failed
>>>> FAILED. Check files in bham
>>>> etc
>>>> No topol.tpr file in kernel334. grompp failed
>>>> FAILED. Check files in kernel334
>>>> 63 out of 63 kernel tests FAILED
>>>> readline() on closed filehandle PIPE at ./gmxtest.pl line 353.
>>>> etc
>>>>
>>>> I've checked the archives and the manual and haven't seen anything 
>>>> relevant to
>>>> this. Any help would be appreciated.
>>>
>>> did you source GMXRC?
>>>>
>>>> Regards
>>>>
>>>> Chris
>>>>
>>>> _______________________________________________
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>>>
>>>
>>> -- 
>>> David van der Spoel, Ph.D.
>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala 
>>> University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205. Fax: 
>>> +4618511755.
>>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>>
>>
>>
>> _______________________________________________
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>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
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>
>


-- 
*******************************************
Chris F. Snook, Ph.D.
X-ray Crystallography Core Manager
Dept. of Biochemistry & Molecular Biology
Medical University of South Carolina
173 Ashley Avenue
Charleston
SC 29425
USA

Phone: 843-792-5848
FAX:843-792-4322
email: snookc at musc.edu
*******************************************