Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Hi Amil, On Mon, Jun 10, 2013 at 11:03 PM, Amil Anderson wrote: > Szilárd, > > I tried the build using a PATH without the Intel compilers and NOT including > the directives -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and it > used the FFTW 3.2 wrappers to MKL. Here is the output fro

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Szilárd, I tried the build using a PATH without the Intel compilers and NOT including the directives -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and it used the FFTW 3.2 wrappers to MKL. Here is the output from mdrun -version: Program: mdrun Gromacs version:VERSION 4.6.1 Precisi

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Szilárd, I just tried the cmake with -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and got a successful build. When I ran the regression tests I got the following results (grepped out the summary lines): All 16 simple tests PASSED All 19 complex tests PASSED All 142 kernel tests PASSED

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

On Mon, Jun 10, 2013 at 6:11 PM, Szilárd Páll wrote: > Amil, > > It looks like there is a mixup in your software configuration and > mdrun is linked against libguide.so, the OpenMP library part of the > Intel compiler v11 which gets loaded early and is probably causing the > crash. This library wa

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

On Mon, Jun 10, 2013 at 4:57 PM, Amil Anderson wrote: > Roland, > > Here is the output from the debug run with the stack trace: > > [aanderson@warp2-login gmxdemo]$ gdb mdrun > GNU gdb Fedora (6.8-27.el5) > Copyright (C) 2008 Free Software Foundation, Inc. > License GPLv3+: GNU GPL version 3 or la

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Amil, It looks like there is a mixup in your software configuration and mdrun is linked against libguide.so, the OpenMP library part of the Intel compiler v11 which gets loaded early and is probably causing the crash. This library was probably pulled in implicitly by MKL which the build system det

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Roland, Here is the output from the debug run with the stack trace: [aanderson@warp2-login gmxdemo]$ gdb mdrun GNU gdb Fedora (6.8-27.el5) Copyright (C) 2008 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Hi, based on Mark's idea I would have thought that the cpu detection would have already failed during cmake. But it seems it detected SSE4.1 correctly. Could you post the stack trace for the crash? (see previous mail for instructions) Roland On Sun, Jun 9, 2013 at 4:42 PM, Amil Anderson wrote:

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Roland, I have posted the cmake output (cmake-4.6.1) and the file CMakeError.log at the usual https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP I see there are some errors but don't know what to make of them. Thanks, Amil -- View this message in context: http://gromacs.5086.x6.nabble.co

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

On Fri, Jun 7, 2013 at 2:06 PM, Mark Abraham wrote: > Running Amil's .tpr, the next output is from our CPU detection machinery. > While the Xeon 5500 is not exactly new, AFAIK there should be no reason for > the detection to fail. But the stack trace will tell. Good point. Amil, please post the cm

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Running Amil's .tpr, the next output is from our CPU detection machinery. While the Xeon 5500 is not exactly new, AFAIK there should be no reason for the detection to fail. But the stack trace will tell. Mark On Fri, Jun 7, 2013 at 7:23 PM, Roland Schulz wrote: > Amil, > > would it be possible

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Amil, would it be possible for you to compile with a different compiler? Ideally gcc 4.7.3. Alternative could you send us the stack for when it crashes? For that you need to: - compile with debug -DCMAKE_BUILD_TYPE=Debug - run under gdb "gdb --arg /path/to/mdrun {your mdrun arguments}" - enter "bt

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Roland, I have now run the regression test on my installation and it all fails for runmd (segmentation fault). Don't see that anything else is being tested. I've placed the output of the make check (Make_check.out) at https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP I'll copy the first