Thanks a lot Mark, that worked (after I did "setenv LD_LIBRARY_PATH
${LD_LIBRARY_PATH}:/usr/people/douglas/programs/gromacs-4.6.3/install/lib").
Quoting Mark Abraham on Fri, 12 Jul 2013
13:22:01 +0100:
On Fri, Jul 12, 2013 at 11:18 AM, Douglas Houston
wrote:
Hi,
I am having trouble in
On Fri, Jul 12, 2013 at 11:18 AM, Douglas Houston
wrote:
> Hi,
>
> I am having trouble installing Gromacs 4.6.3.
>
> In bash I am using the following sequence of commands:
>
> cd gromacs-4.6.3
> mkdir build
> cd build
> CC=/usr/people/douglas/programs/gcc-4.7.3/installation/bin/gcc
> ~/programs/cm
Hi,
I am having trouble installing Gromacs 4.6.3.
In bash I am using the following sequence of commands:
cd gromacs-4.6.3
mkdir build
cd build
CC=/usr/people/douglas/programs/gcc-4.7.3/installation/bin/gcc
~/programs/cmake-2.8.7/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
make
sudo make install
Ev
On 29/05/2012 3:09 PM, a a wrote:
Dear Sir/Madam,
Follow the steps below, I have installed fftw library and gromacs as a
root.
(1) tar -xzvf fftw-3.0.1.tar.gz
(2) cd fftw-3.0.1
(3) ./configure --enable-float --enable-threads --enable-shared
Here you enabled threads for fftw, which is not re
Dear Sir/Madam,
Follow the steps below, I have installed fftw library and gromacs as a root.
(1) tar -xzvf fftw-3.0.1.tar.gz(2) cd fftw-3.0.1(3) ./configure --enable-float
--enable-threads --enable-shared(4) make(5) make install(6) tar -xzvf
gromacs-4.5.5.tar.gz(7) cd gromacs-4.5.5(8) ./confi
Hi everyone, I met a problem in the installation of gromacs-4.5. There isn’t any mistake in the configuration step, but in the “make” step, it exit with the error: make[4]: *** No rule to make target `/usr/incluDe/gnu/stubs-64.h', needed by `sgetri.lo'. Stop. make[4]: Leaving directory `/home/md
hey thanks Sander for bringing my attention to -nt option.. ;)
--
sikandar
On Thu, Oct 14, 2010 at 6:08 AM, Sander Pronk wrote:
>
> On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote:
>
> > Recently I installed gromacs4.5.1 without mpi support on my workstation
> with 8 cores using cmake and m
On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote:
> Recently I installed gromacs4.5.1 without mpi support on my workstation with
> 8 cores using cmake and make -j 8, make install commands ( as suggested on
> installation instructions).
>
> Now when I do mdrun it automatically utilizes all t
.csh: line 8: `if (!
>>> $?LD_LIBRARY_PATH)
>>> setenv
>>> LD_LIBRAR
>>> Y_PATH ""'
>>> [r...@xxx bin]#
>>>
>>> This do
gt; unexpected token `setenv '
>>> /local/gromacs/bin/GMXRC.csh: line 8: `if (!
>>> $?LD_LIBRARY_PATH)
>>> setenv
>>> LD_LIBRAR
>>> Y_PATH ""&#
t;>
<mailto:sathisbioi...@gmail.com <mailto:sathisbioi...@gmail.com>
<mailto:sathisbioi...@gmail.com
<mailto:sathisbioi...@gmail.com>>>>
Date: Wednesday, October 13, 2010 14:31
Subject:
This doesn't work, and shouldn't.
>>
>> And the only thing you should be doing as root are "make
>> install"
>> and "make links" (if you want the latter). Otherwise you'll
>> trash
>> your system b
<mailto:mark.abra...@anu.edu.au>>> wrote:
- Original Message -
From: Sathish mailto:sathisbioi...@gmail.com>
<mailto:sathisbioi...@gmail.com
<mailto:sathisbioi...@gmail.com>>>
>>>
>>And the only thing you should be doing as root are "make install"
>>and "make links" (if you want the latter). Otherwise you'll trash
>>your system before you know what you've done.
>>
>>Mark
>>
>
to fix this problem and luck is not working.
It should, if the "source" command worked.
Mark
On Wed, Oct 13, 2010 at 12:57 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:
- Original Message -
From: Sathish mailto:sathisbio
should, if the "source" command worked.
>
> Mark
>
>
>
>
>
> On Wed, Oct 13, 2010 at 12:57 PM, Mark Abraham wrote:
>
>>
>>
>> - Original Message -
>> From: Sathish
>> Date: Wednesday, October 13, 2010 14:31
>> Subject: [gmx
problem and luck is not working.
It should, if the "source" command worked.
Mark
On Wed, Oct 13, 2010 at 12:57 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:
- Original Message -----
From: Sathish mailto:sathisbioi...@gmail.com>>
Date:
ioi...@gmail.com>>
Date: Wednesday, October 13, 2010 14:31
Subject: [gmx-users] Gromacs installation problem @ RHEL5.5 server
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
> Dear all,
> I have compiled and installed gromacs 4.5.1 on RHEL5.5 server
Sathish
> Date: Wednesday, October 13, 2010 14:31
> Subject: [gmx-users] Gromacs installation problem @ RHEL5.5 server
> To: gmx-users@gromacs.org
>
> > Dear all,
> > I have compiled and installed gromacs 4.5.1 on RHEL5.5 server. I have
> also installed openmpi-1.2.8, fftw
- Original Message -
From: Sathish
Date: Wednesday, October 13, 2010 14:31
Subject: [gmx-users] Gromacs installation problem @ RHEL5.5 server
To: gmx-users@gromacs.org
> Dear all,
> I have compiled and installed gromacs 4.5.1 on RHEL5.5 server. I have also
> installed open
Dear all,
I have compiled and installed gromacs 4.5.1 on RHEL5.5 server. I have also
installed openmpi-1.2.8, fftw-3.2.2 and gsl-1.11. After gromacs 4.5.1
installation did make tests and make links. Finally got message "GROMACS is
installed under /root/software" and "binary executable installed
/u
- Original Message -
From: Sanku M
Date: Monday, May 31, 2010 13:00
Subject: [gmx-users] gromacs installation problem in ibm powerpc system
To: gmx-users@gromacs.org
> Hi,> I am having a problem in a cluster which is IBM PowerPC 970MPs and
> running SUSE linux and it has
Hi,
I am having a problem in a cluster which is IBM PowerPC 970MPs and running
SUSE linux and it has IBM XL C & Fortran compliers ( xlf, xlc ).
I was trying to install gromacs 4 there using open-mpi which is already
installed using ibm compilers.
Here is my configure command:
./configure --p
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