Hi,
I want to compile GROMACS to support CUDA.
First I do a cmake:
CMAKE_PREFIX_PATH=/scratch/ihpc/ihpczidj/local/bin/:/usr/local/CUDA/5.0/
cmake ../gromacs-4.6 -DGMX_GPU=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF
-DGMX_OPENMP=ON -DBUILD_SHARED_LIBS=OFF
-DCMAKE_INSTALL_PREFIX=/scratch/ihpc/ihpczidj/
Dear all,
I'm facing a problem when compiling Gromacs. This is the message I got:
numa_malloc.c:117:73: error: expected ‘)’ before ‘Processor’
numa_malloc.c:118:78: error: expected ‘)’ before ‘ProcNumber’
numa_malloc.c:121:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ be
I've never worked with such architecture, but I do remember seeing a few posts
in the past, some of which may be useful. Perhaps this one will hold some clues:
http://lists.gromacs.org/pipermail/gmx-users/2007-April/027074.html
Sorry I can't provide much more than this, but I thought I'd at
Hello again
I followed your advices this time
here's what I did :
downloading gromacs 4.0.7
downloading fftw 2.1.5
initializing environment variables (modified to fit my configuration
(pwr5) :
export LDFLAGS='-L/usr/local/lib'
export CPPFLAGS='-I/usr/local/include'
export
PATH=/usr/lpp/pp
Dear Sebastien:
Perhaps it's obvious, but can you confirm that you used the compilation
options that I posted? My suggestion was not so much that you should try
to compile 4.0.4 but that you should try the options that I posted. So
if you used your original compilation commands with gromacs ve
Hi Chris.
Thank you for your answer
I tried the 4.0.4 version but unfortunately, it did better but new
errors appeared anyway
so what I test now is another version of FFTW (fftw-2.1.5.tar.gz)
and the "make" command for gromacs 4.0.7 was a success
so the question is : What will be the differe
This worked for me on AIX 5.3 for gromacs 4.0.4, I didn't try to
compile any gromacs versions after that because we found that gromacs
runs much better on Xeons and Opterons than it runs on power6's
running AIX 5.3
If you have a problem specific to 4.0.7 (i.e. you can compile 4.0.4
alrigh
Dear All,
I have problems with Compiling Gromacs 4.0.7 on AIX 5.3
using gromacs 4.0.7 and fftw 3.2.2
here is what I do for FFTW :
./configure --enable-float
make
make install
everything works fine
after that, I do some variable settings :
export CC='xlc_r'
export F77='xlf_r'
export FFL
Pedro Alberto Valiente Flores wrote:
Hi:
I am trying to compile gromacs 4.03_mpi in ubuntu hardy.
I use this comand-line:
./configure --enable-mpi --prefix=$HOME/software/gmx403 MPICC=
$HOME/software/openmpi/bin/mpicc CPPFLAGS="-I
$HOME/software/openmpi/include -I$HOME/software/fftw/include/"
Hi:
I am trying to compile gromacs 4.03_mpi in ubuntu hardy.
I use this comand-line:
./configure --enable-mpi --prefix=$HOME/software/gmx403 MPICC=
$HOME/software/openmpi/bin/mpicc CPPFLAGS="-I
$HOME/software/openmpi/include -I$HOME/software/fftw/include/"
LDFLAGS="-L$HOME/software/openmpi/lib -L$
Mike Hanby wrote:
Howdy,
I'd like to use "--with-external-blas --with-external-lapack
--with-fft=fftw3 --with-gsl" and the Intel v10.1 compilers on a Linux
(Centos 5 x86_64) system.
My question, do I first need to compile blas, lapack, fftw3 and gsl
using the Intel compilers, or will the librar
Howdy,
I'd like to use "--with-external-blas --with-external-lapack
--with-fft=fftw3 --with-gsl" and the Intel v10.1 compilers on a Linux
(Centos 5 x86_64) system.
My question, do I first need to compile blas, lapack, fftw3 and gsl
using the Intel compilers, or will the libraries that are already
> I had trouble compiling gromacs-3.3.1 parallel (but not serial) on
> itanium2 until I found the following post:
>
> http://www.gromacs.org/pipermail/gmx-users/2004-February/009171.html
>
> And that solution was good... I now have a functional executable.
>
> To clarify, the solution was to do thi
I had trouble compiling gromacs-3.3.1 parallel (but not serial) on
itanium2 until I found the following post:
http://www.gromacs.org/pipermail/gmx-users/2004-February/009171.html
And that solution was good... I now have a functional executable.
To clarify, the solution was to do this:
export
D] On Behalf Of Ivano Eberini
Sent: Friday, October 12, 2007 05:31
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Compiling GROMACS with FORTRAN?
Il giorno 12/ott/07, alle ore 11:29, David van der Spoel ha scritto:
> Ivano Eberini wrote:
>> Dear all,
>> we have just instal
Il giorno 12/ott/07, alle ore 11:29, David van der Spoel ha scritto:
Ivano Eberini wrote:
Dear all,
we have just installed GROMACS-3.3.2 on a BlueGene (BG/L) cluster,
compiling it without FORTRAN.
Do you deem it could be better to recompile it adding "--enable-
fortran"?
the proof of the pu
Ivano Eberini wrote:
Dear all,
we have just installed GROMACS-3.3.2 on a BlueGene (BG/L) cluster,
compiling it without FORTRAN.
Do you deem it could be better to recompile it adding "--enable-fortran"?
the proof of the pudding is in the eating.
please try it.
Thanks in advance for any sugg
Dear all,
we have just installed GROMACS-3.3.2 on a BlueGene (BG/L) cluster,
compiling it without FORTRAN.
Do you deem it could be better to recompile it adding "--enable-
fortran"?
Thanks in advance for any suggestion.
Best regards,
Ivano
--
Ivano Eberini
Gruppo di Studio per la Proteomica
Kedar Potdar wrote:
I think, i forgot to mention that i am trying to compile GROMACS on
native windows and not on Cygwin...
That's going to make it hard to interest people in helping you, since
probably nobody has done that before, and with the availability of
cygwin few people have an incent
I think, i forgot to mention that i am trying to compile GROMACS on native
windows and not on Cygwin...
On 5/17/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
Kedar Potdar wrote:
> Hi guys,
>
> I am trying to compiler GROMACS onto 64 bit windows platform with AMD
> Opteron Machine with Windows 200
Kedar Potdar wrote:
Hi guys,
I am trying to compiler GROMACS onto 64 bit windows platform with AMD
Opteron Machine with Windows 2003 Server R2.
It may sound pretty basic but i am not able to figure out...
I could see assembly code in nonbonded directory and i am trying to
write makefile t
Hi guys,
I am trying to compiler GROMACS onto 64 bit windows platform with AMD
Opteron Machine with Windows 2003 Server R2.
It may sound pretty basic but i am not able to figure out...
I could see assembly code in nonbonded directory and i am trying to write
makefile to build the same but i am
Shall be the same as linux. But locate first where the FFTW's include
and lib are. And add them respectively in
CFLAGS=-I{include}
LDFLAGS=-L{lib}
Yang Ye
Vanessa Oklejas wrote:
Hi All,
I want to get gromacs v 3.1.0 running on my PC via cygwin. I have
been able to compile fftw-3.0.1 but, w
l 14, 2006 8:02 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] compiling gromacs with cygwin
>
>
> Hi All,
>
> I want to get gromacs v 3.1.0 running on my PC via cygwin. I have
> been able to compile fftw-3.0.1 but, when I try to execute the
> conf
I'm pretty sure that GROMACS prior to version 3.3 requires FFTW
version 2 and won't work with FFTW 3. 3.3 and later are compatible
with either version.
David
On 4/13/06, Vanessa Oklejas <[EMAIL PROTECTED]> wrote:
> Hi All,
>
> I want to get gromacs v 3.1.0 running on my PC via cygwin. I have
>
Hi All,
I want to get gromacs v 3.1.0 running on my PC via cygwin. I have
been able to compile fftw-3.0.1 but, when I try to execute the
configure file, it terminates when it tries (unsuccessfully) to find
the fftw library. Anyone have experience with this?
Thanks,
Vanessa
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