Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Albert
On 07/04/2013 07:59 PM, Mark Abraham wrote: I plan to release 4.6.3 tomorrow, once I've gotten some more urgent stuff off my plate:-). Mark thanks a lot for kind messages, Mark. It seems that Gromacs update more and more frequently Albert -- gmx-users mailing listgmx-users@gromacs.o

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Mark Abraham
I plan to release 4.6.3 tomorrow, once I've gotten some more urgent stuff off my plate :-). Mark On Thu, Jul 4, 2013 at 7:47 PM, Albert wrote: > On 07/04/2013 05:52 PM, Szilárd Páll wrote: >> >> FYI: 4.6.2 contains a bug related to thread affinity setting which >> will lead to a considerable per

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Albert
On 07/04/2013 05:52 PM, Szilárd Páll wrote: FYI: 4.6.2 contains a bug related to thread affinity setting which will lead to a considerable performance loss (I;ve seen 35%) as well as often inconsistent performance - especially with GPUs (case in which one would run many OpenMP threads/rank). My a

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Szilárd Páll
FYI: 4.6.2 contains a bug related to thread affinity setting which will lead to a considerable performance loss (I;ve seen 35%) as well as often inconsistent performance - especially with GPUs (case in which one would run many OpenMP threads/rank). My advice is that you either use the code from git

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Albert
On 07/04/2013 11:18 AM, Mark Abraham wrote: No idea. I do not think there is any need for you to use BUILD_SHARED_LIBS=OFF, and it could well be the problem. Mark thank you all the same. I found the problem, there is a subdirectory in cuda5.0: /export/cuda5.0/cuda the problem solved after I

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Mark Abraham
No idea. I do not think there is any need for you to use BUILD_SHARED_LIBS=OFF, and it could well be the problem. Mark On Thu, Jul 4, 2013 at 11:07 AM, Albert wrote: > On 07/04/2013 10:43 AM, Oliver Schillinger wrote: >> >> It seems that GROMACS is looking for a shared library, but you compiled

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Albert
On 07/04/2013 10:43 AM, Oliver Schillinger wrote: It seems that GROMACS is looking for a shared library, but you compiled FFTW statically (--enable-static). Either recompile FFTW --enable-shared or link GROMACS statically by passing -DBUILD_SHARED_LIBS=OFF to cmake. Hello guys: thanks a l

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Mark Abraham
On Thu, Jul 4, 2013 at 10:31 AM, Mark Abraham wrote: > On Thu, Jul 4, 2013 at 9:09 AM, Albert wrote: >> Hello: >> >> I am trying to compile Gromacs-4.6.2 for a GPU cluster with following >> command: >> >> >> CC=icc FC=ifort F77=ifort CXX=icpc >> CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Mark Abraham
On Thu, Jul 4, 2013 at 10:43 AM, Oliver Schillinger wrote: > It seems that GROMACS is looking for a shared library, but you compiled FFTW > statically (--enable-static). Either recompile FFTW --enable-shared or link > GROMACS statically by passing -DBUILD_SHARED_LIBS=OFF to cmake. The FindFFTW.cm

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Oliver Schillinger
It seems that GROMACS is looking for a shared library, but you compiled FFTW statically (--enable-static). Either recompile FFTW --enable-shared or link GROMACS statically by passing -DBUILD_SHARED_LIBS=OFF to cmake. On our cluster I had problems compiling the MPI version of GROMACS with dynam

Re: [gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Mark Abraham
On Thu, Jul 4, 2013 at 9:09 AM, Albert wrote: > Hello: > > I am trying to compile Gromacs-4.6.2 for a GPU cluster with following > command: > > > CC=icc FC=ifort F77=ifort CXX=icpc > CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4 > cmake .. -DGMX_MPI=ON -DCMAKE_INS

[gmx-users] fftw compile error for 4.6.2

2013-07-04 Thread Albert
Hello: I am trying to compile Gromacs-4.6.2 for a GPU cluster with following command: CC=icc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON -