<br> Thanks for clarifying my doubts. I have started to run demo its working. I have checked processor speed its says only one cpu is running for that program (pdb2gmx). my server configuration (RHEL 5.5) is 2 processor with 6 core, totally 24 processor. I have set "export NCPU=24" while installing gromacs. Could you tell me how to run gromacs with all processor ?<br>
<br><pre><br></pre> <br><br><br><div class="gmail_quote">On Wed, Oct 13, 2010 at 8:24 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
Sathish wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
Dear Mark,<br>
<br>
wow its working. Thank you lot.. As per installation instruction gromacs installed successfully and demo also working.<br>
Then i have downloaded test set "gmxtest-4.0.4.tgz". While running i got error message like this,<br>
<br></div>
[root@XXX gmxtest]# ./<a href="http://gmxtest.pl" target="_blank">gmxtest.pl</a> <<a href="http://gmxtest.pl" target="_blank">http://gmxtest.pl</a>> all<div><div></div><div class="h5"><br>
FAILED. Check files in angles1<br>
FAILED. Check files in angles125<br>
FAILED. Check files in bham<br>
FAILED. Check files in bonds1<br>
FAILED. Check files in bonds125<br>
FAILED. Check files in dih1<br>
FAILED. Check files in dih125<br>
FAILED. Check files in g96angles1<br>
FAILED. Check files in g96angles125<br>
FAILED. Check files in g96bonds1<br>
FAILED. Check files in g96bonds125<br>
FAILED. Check files in imp1<br>
FAILED. Check files in imp36<br>
FAILED. Check files in morse<br>
FAILED. Check files in rb1<br>
FAILED. Check files in rb125<br>
16 out of 16 simple tests FAILED<br>
FAILED. Check files in acetonitrilRF<br>
FAILED. Check files in aminoacids<br>
FAILED. Check files in argon<br>
FAILED. Check files in butane<br>
FAILED. Check files in dec+water<br>
FAILED. Check files in ethyleenglycol<br>
FAILED. Check files in fe_test<br>
FAILED. Check files in field<br>
FAILED. Check files in nacl<br>
FAILED. Check files in sw<br>
FAILED. Check files in tip4p<br>
FAILED. Check files in tip4pflex<br>
FAILED. Check files in urea<br>
FAILED. Check files in water<br>
14 out of 14 complex tests FAILED<br>
FAILED. Check files in kernel020<br>
FAILED. Check files in kernel120<br>
FAILED. Check files in kernel121<br>
FAILED. Check files in kernel122<br>
FAILED. Check files in kernel123<br>
FAILED. Check files in kernel124<br>
FAILED. Check files in kernel220<br>
FAILED. Check files in kernel221<br>
FAILED. Check files in kernel222<br>
FAILED. Check files in kernel223<br>
FAILED. Check files in kernel224<br>
FAILED. Check files in kernel320<br>
FAILED. Check files in kernel321<br>
FAILED. Check files in kernel322<br>
FAILED. Check files in kernel323<br>
FAILED. Check files in kernel324<br>
16 out of 63 kernel tests FAILED<br>
Error not all 45 pdb2gmx tests have been done successfully<br>
Only 9 energies in the log file<br>
[root@XXX gmxtest]#<br>
Could you explain what is exact problem and how to solve it?<br>
<br>
</div></div></blockquote>
<br>
1. The test set is not very robust, so failures are not necessarily indicative of any actual problem.<br>
2. You're using the 4.0.4 test set with version 4.5.1, so some failures are probably due to new command line options, etc. (especially in the case of pdb2gmx) being necessary but not invoked.<br>
<br>
As it stands, there is no effective way to test the validity of a Gromacs installation.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<br>
On Wed, Oct 13, 2010 at 6:15 PM, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br>
On 2010-10-13 10.54, Sathish wrote:<br>
<br>
Dear Mark,<br>
<br>
I have one more doubt. How to run "luck". If i run luck<br>
anywhere its says command not found..<br>
my installed and binary directory cant find luck program. how to do?<br>
without checking luck shall i start to run demo?<br>
<br>
Instructions are outdated. The program is now called g_luck<br>
<br>
<br>
<br>
On Wed, Oct 13, 2010 at 3:19 PM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>> wrote:<br>
<br>
On 13/10/2010 5:01 PM, Mark Abraham wrote:<br>
<br>
On 13/10/2010 4:55 PM, Sathish wrote:<br>
<br>
Dear Mark,<br>
Thanks for your reply. In my server gromacs<br>
installed at<br>
"local/gromacs". I have checked out point 8 as you<br>
mentioned.<br>
It was working with this "source<br>
/local/gromacs/bin/GMXRC" command.<br>
<br>
<br>
That's all you need to do, in every shell from which you<br>
want to<br>
use GROMACS. Or, put that command in your shell login scripts<br>
(Google for details).<br>
<br>
and also tried , entered "local/gromacs/bin" path and<br>
calling to<br>
GMXRC but it shows error<br>
<br>
[root@xxx bin]# GMXRC<br>
/local/gromacs/bin/GMXRC: line 35: return: can only<br>
`return' from<br>
a function<br>
or<br>
sourced script<br>
/local/gromacs/bin/GMXRC: line 44: CSH:: command not<br>
found<br>
/local/gromacs/bin/GMXRC.csh: line 8: syntax error near<br>
unexpected token `setenv '<br>
/local/gromacs/bin/GMXRC.csh: line 8: `if (!<br>
$?LD_LIBRARY_PATH)<br>
setenv<br>
LD_LIBRAR<br>
Y_PATH ""'<br>
[root@xxx bin]#<br>
<br>
This doesn't work, and shouldn't.<br>
<br>
And the only thing you should be doing as root are "make install"<br>
and "make links" (if you want the latter). Otherwise you'll trash<br>
your system before you know what you've done.<br>
<br>
Mark<br>
<br>
<br>
kindly help me to fix this problem and luck is not<br>
working.<br>
<br>
It should, if the "source" command worked.<br>
<br>
Mark<br>
<br>
<br>
<br>
<br>
<br>
On Wed, Oct 13, 2010 at 12:57 PM, Mark Abraham<br>
<<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>>> wrote:<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: Sathish <<a href="mailto:sathisbioinfo@gmail.com" target="_blank">sathisbioinfo@gmail.com</a><br>
<mailto:<a href="mailto:sathisbioinfo@gmail.com" target="_blank">sathisbioinfo@gmail.com</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:sathisbioinfo@gmail.com" target="_blank">sathisbioinfo@gmail.com</a><br>
<mailto:<a href="mailto:sathisbioinfo@gmail.com" target="_blank">sathisbioinfo@gmail.com</a>>>><br>
Date: Wednesday, October 13, 2010 14:31<br>
Subject: [gmx-users] Gromacs installation problem<br>
@ RHEL5.5<br>
server<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<br>
> Dear all,<br>
> I have compiled and installed gromacs 4.5.1 on<br>
RHEL5.5<br>
server. I have also installed openmpi-1.2.8,<br>
fftw-3.2.2 and<br>
gsl-1.11. After gromacs 4.5.1 installation did<br>
make tests and<br>
make links. Finally got message "GROMACS is<br>
installed under<br>
/root/software" and "binary executable installed<br>
/usr/local/bin". Utill this am not getting any<br>
errors.<br>
> Then i was tried to calling "luck" but get<br>
"command not<br>
found".I have searched the forum it says binary<br>
executable<br>
not in your path.<br>
> Am installing first time and need to know PATH<br>
is right<br>
which i given? Could anybody help me to solve<br>
this problem?<br>
> Advance thanks..<br>
<br>
Check out point 8 of<br>
<a href="http://www.gromacs.org/Downloads/Installation_Instructions" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions</a><br>
<br>
Mark<br>
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Regards,<br>
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<br>
<br>
<br>
-- David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br></div>
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</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
-- <br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>-- <br>Regards,<br>N. Sathishkumar,<br><br>