Please test using the test set version that matches the code! On Sep 4, 2013 5:16 AM, "Guanglei Cui" <amber.mail.arch...@gmail.com> wrote:
> Hi Szilard, > > Thanks for your reply. I may try your suggestions tomorrow when I get back > to work. > > Feeling curious, I downloaded and compiled gmx 4.6.3 on my home computer > (gcc-4.6.3 and ubuntu 12.04). Even with the default (below), kernel (38 out > of 142) and freeenergy (2 out of 9) tests would still fail. I'm not sure > what is going on. Perhaps I should try an earlier version that matches the > regressiontests? > > cmake .. -DGMX_BUILD_OWN_FFTW=on > -DREGRESSIONTEST_PATH=/home/cuigl/Downloads/regressiontests-4.6.1 > > Regards, > Guanglei > > > On Tue, Sep 3, 2013 at 7:40 PM, Szilárd Páll <szilard.p...@cbr.su.se> > wrote: > > > 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 > > > > > > -- > 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
