RE: [gmx-users] Building Single and Double Precision in 4.6.1?

[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Szilárd Páll Sent: Thursday, April 18, 2013 12:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Building Single and Double Precision in 4.6.1? On Thu, Apr 18, 2013 at 6:17 PM, Mike Hanby mha...@uab.edu wrote: Thanks for the reply, so

RE: [gmx-users] Building Single and Double Precision in 4.6.1?

Subject: Re: [gmx-users] Building Single and Double Precision in 4.6.1? That's best. GROMACS will take care of a _d suffix for double precision for you. Mark On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote: Howdy, What's the proper procedure for building both single and double

[gmx-users] Building Single and Double Precision in 4.6.1?

Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \

RE: [gmx-users] GROMACS on Bluegene

Has there been any further discussion about fixing the issues discussed below regarding Blue Gene? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, October 16, 2008 10:43 PM To: Gromacs Users Subject: [gmx-users] GROMACS on

RE: [gmx-users] FFTW problem for Gromacs4

Also, I'm not positive, but I believe the switch should be --enable-float not --enable-floats, so your fftw compile probably didn't build the float version. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jussi Lehtola Sent: Tuesday, November 11, 2008

RE: [gmx-users] Gromacs 4 Scaling Benchmarks...

The fftw used during compilation was FFTW 3.1.2 compiled using the GNU compilers. From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Yawar JQ Sent: Sunday, November 09, 2008 3:31 PM To: gmx-users@gromacs.org Subject: [gmx-users] Gromacs 4 Scaling Benchmarks... I was wondering

[gmx-users] Test Set for Gromacs 4?

Is there a test set available for Gromacs 4? I looked here and found 3.3.2 and 3.3.3: ftp://ftp.gromacs.org/pub/tests/ Thanks, Mike ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] Compiling Gromacs 4 using Intel Compilers

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

[gmx-users] Gromacs 4 SRC RPM?

Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up on: ftp://ftp.gromacs.org/pub/gromacs/rpm Thanks, Mike ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

RE: [gmx-users] Gromacs 4 SRC RPM?

for GROMACS users Subject: Re: [gmx-users] Gromacs 4 SRC RPM? On Fri, 2008-10-24 at 09:06 -0500, Mike Hanby wrote: Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up on: ftp://ftp.gromacs.org/pub/gromacs/rpm You may be able to use the one in Fedora, e.g. http

[gmx-users] Blue Gene Compile - Gromacs 4

Howdy, I'm looking at compiling Gromacs 4 for the Blue Gene/L and am stuck at the compilation of the prerequisite FFTW 3.1.3. If anyone out there has successfully cross compiled FFTW and Gromacs for the Blue Gene, would you mind sharing your settings used to run the ./configure scripts?

RE: [gmx-users] Compiling GROMACS with FORTRAN?

Howdy Ivano, Would you mind sharing the steps used to compile Gromacs on the BlueGene/L? I've tried this several times with the IBM cross compilers and always end up failing. Thanks for any information, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On

[gmx-users] Blue Gene compilation error cannot compute sizeof (int) 77

Howdy, I'm getting an error while running configure for Gromacs 3.3.1 on Blue Gene. checking size of int... configure: error: cannot compute sizeof (int), 77 I've searched the archives but haven't found anything that resolves the problem. I'm cross compiling this on the front end

[gmx-users] Compile Gromacs for Blue Gene/L

Howdy, We are bringing a one rack (1024 node) IBM Blue Gene/L system online. I've been tasked with compiling Gromacs for the Blue Gene. We have the XL compilers installed (blrts_xlc / mpixlc, etc), so I'll be using those rather than GNU. Has anyone on here successfully cross compiled

[gmx-users] compile Gromacs 3.2.1: line 0: unexpected EOF while looking for matching `'

I'm trying to compile Gromacs 3.2.1 (a user requested this version specifically). The configure succeeds, however make fails with: /bin/sh: -c: line 0: unexpected EOF while looking for matching `' /bin/sh: -c: line 1: syntax error: unexpected end of file The system is a 64bit RHEL 4

[gmx-users] RE: Gromacs 3.2.1: catastrophic error: could not open source file sfftw.h

/gromacs-3.2.1/src' make: *** [all-recursive] Error 1 -Original Message- From: Mike Hanby Sent: Friday, January 19, 2007 8:26 AM To: 'Discussion list for GROMACS users' Subject: Gromacs 3.2.1: catastrophic error: could not open source file sfftw.h Sorry if this gets posted twice, I emailed

[gmx-users] Gromacs 3.2.1: catastrophic error: could not open source file sfftw.h

Sorry if this gets posted twice, I emailed it 18 hours ago and don't see it on the list. Howdy, One of my users requested that I compile Gromacs 3.2.1 on our system. I've already compiled and installed 3.3.1 and 3.3 on this system. When I compile 3.2.1, I get the error during config:

[gmx-users] Gromacs 3.2.1: catastrophic error: could not open source file sfftw.h

Howdy, One of my users requested that I compile Gromacs 3.2.1 on our system. I've already compiled and installed 3.3.1 and 3.3 on this system. When I compile 3.2.1, I get the error during config: 'catastrophic error: could not open source file sfftw.h' At first I figured Gromacs 3.2.1 must

RE: [gmx-users] Gromacs 3.2.1: catastrophic error: could not opensource file sfftw.h

: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mike Hanby Sent: Thursday, January 18, 2007 2:44 PM To: Discussion list for GROMACS users Subject: [gmx-users] Gromacs 3.2.1: catastrophic error: could not opensource file sfftw.h Howdy, One of my users requested that I compile Gromacs 3.2.1

[gmx-users] Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)

Howdy, a user of a cluster that I manage sent me an output file of their Gromacs 3.3.1 job. It looks like the job runs for approx 11 hours and then abruptly terminates with a SEGV_MAPERR. What could cause this (gromacs, or a system config / resource?). The output of the log file is below, thanks