On Tue, Sep 3, 2013 at 9:50 PM, Guanglei Cui <amber.mail.arch...@gmail.com> wrote: > Hi Mark, > > I agree with you and Justin, but let's just say there are things that are > out of my control ;-) I just tried SSE2 and NONE. Both failed the > regression check.
That's alarming, with GMX_CPU_ACCELERATION=None only the plain C kernels get compiled which should pass the regressiontests even with icc 11 - although I have not tried myself. Some things that don't take much time and may be useful to try: - make sure that when GMX_CPU_ACCELERATION=None the resulting binary does not get compiled with flags that instruct the compiler to auto-generate SSE4.1 code (e.g. -msse4.1 or -xHOST); - run with the GMX_NOOPTIMIZEDKERNELS environment variable set which disables the architecture-specific kernels at runtime (regardless of what mdrun was compiled with); the end result should be the same as above: the plain C kernels should be used (although with GMX_CPU_ACCELERATION != None the instructions of requested instruction set will be generated by the compiler as an optimization). -- Szilárd > I think I've spent enough time on this, which justifies > escalating this to someone with the control, but is failing regression > check with no CPU/instruction optimization normal? > > Regards, > Guanglei > > > On Tue, Sep 3, 2013 at 3:35 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > >> On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui >> <amber.mail.arch...@gmail.com> wrote: >> > Dear GMX users, >> > >> > I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver >> > 11.x). Here is how I compiled FFTW, >> > >> > ./configure CC=icc F77=ifort CFLAGS="-O3 -gcc" >> > --prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads >> --enable-threads >> > --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float >> >> I can't imagine you'll benefit from threaded FFTW, but feel free to try... >> >> > And, here is how I invoked cmake, >> > >> > CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 >> > >> -DFFTWF_LIBRARY=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/lib/libfftw3f.a >> > >> -DFFTWF_INCLUDE_DIR=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/include >> > -DBUILD_SHARED_LIBS=no >> > >> -DCMAKE_INSTALL_PREFIX=/home/gc603449/APPLICATIONS/gromac-4.6.3/thread-float-static >> > -DREGRESSIONTEST_PATH=/tmp/gromacs-4.6.3/regressiontests-4.6.1 >> > >> > When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of >> 9 >> > free energy tests failed. >> > >> > This is my first time to compile gromacs, which I am not very familiar >> > with. I wonder if anyone can kindly point out what has gone wrong, and >> > where to look for hints. Any help is much appreciated. >> >> As Justin said, get an up-to-date compiler. gcc regularly outperforms >> icc, anyway. You can use cmake -DGMX_CPU_ACCELERATION=SSE2 to get a >> least-common-denominator build, but if you care about threaded FFTW >> then you care enough to get a new compiler! >> >> Mark >> >> > Best regards, >> > -- >> > Guanglei Cui >> > PS: I am aware of a warning about using older Intel compilers with 4.6.3, >> > but that's the only quality compiler I got. The gcc compiler I have >> access >> > to is too old (ver 4.1.x) >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > * Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Guanglei Cui > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
