[gmx-users] (no subject)

[Justin A. Lemkul]

Kwee Hong wrote:
> Hi. When I was trying to do the test run for my installed gromacs, I got 
> message below return to me even though i've source GMXRC (source 
> /usr/local/gromacs/bin/GMXRC). Can some one tell me why? Thanks.
> 

"Permission denied" means you're not allowed to write files to those directories 
(you need admin privileges, i.e. sudo to do so).  If the test script can't write 
files, then all of the tests will fail.

-Justin

> bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl all                   
> 102 out of 102 simple tests FAILED
> sh: grompp.out: Permission denied
> No topol.tpr file in bin. grompp failed
> FAILED. Check files in bin
> sh: grompp.out: Permission denied
> No topol.tpr file in include. grompp failed
> FAILED. Check files in include
> sh: grompp.out: Permission denied
> No topol.tpr file in lib. grompp failed
> FAILED. Check files in lib
> sh: grompp.out: Permission denied
> No topol.tpr file in share. grompp failed
> FAILED. Check files in share
> 4 out of 4 complex tests FAILED
> sh: grompp.out: Permission denied
> No topol.tpr file in OpenSourceLicenses. grompp failed
> FAILED. Check files in OpenSourceLicenses
> sh: grompp.out: Permission denied
> No topol.tpr file in OpenSourceVersions. grompp failed
> FAILED. Check files in OpenSourceVersions
> sh: grompp.out: Permission denied
> No topol.tpr file in bin. grompp failed
> FAILED. Check files in bin
> sh: grompp.out: Permission denied
> No topol.tpr file in gromacs. grompp failed
> FAILED. Check files in gromacs
> sh: grompp.out: Permission denied
> No topol.tpr file in i386-mingw32-3.4.5. grompp failed
> FAILED. Check files in i386-mingw32-3.4.5
> sh: grompp.out: Permission denied
> No topol.tpr file in include. grompp failed
> FAILED. Check files in include
> sh: grompp.out: Permission denied
> No topol.tpr file in info. grompp failed
> FAILED. Check files in info
> sh: grompp.out: Permission denied
> No topol.tpr file in lib. grompp failed
> FAILED. Check files in lib
> sh: grompp.out: Permission denied
> No topol.tpr file in share. grompp failed
> FAILED. Check files in share
> 9 out of 9 kernel tests FAILED
> Opening pdb2gmx.log for writing at ./gmxtest.pl line 300.
> 
> Regards..
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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