Re: [gmx-users] Error: Cannot find AVX 512F compiler flag
It's work okay after I add to the $PATH: /opt/rh/devtoolset-6/root/usr/bin/gcc Thanks Shlomit On 16/01/2020, 11:23, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" wrote: That tells you what your CPU is capable of. We need to know whether cmake has found the compiler that can issue the instructions. Follow the suggestions Roland and I have made. Mark On Wed, 15 Jan 2020 at 10:45, Shlomit Afgin wrote: > > > I ran: > > cat /proc/cpuinfo | grep -i avx512 > > > > and got: > > avx512f avx512dq avx512cd avx512bw avx512vl > > > > So I thought I can use it. Am I wrong? > > > > Shlomit > > > > On 15/01/2020, 11:14, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Szilárd Páll" < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > pall.szil...@gmail.com> wrote: > > > > Hi, > > > > What hardware are you targeting? Unless you need AVX512 support, you > could > > just manually specify the appropriate setting in GMX_SIMD, e.g. > > -DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 > is not > > supported. > > > > Cheers, > > -- > > Szilárd > > > > > > On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin < > shlomit.af...@weizmann.ac.il> > > wrote: > > > > > > > > Hi, > > > I tried to install GROMACS 2019.5 on CentOS7, > > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > > > > > I have already installed devtoolset-6 and still get this error: > > > > > > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS > > > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed > > > -- Could not find any flag to build test source (this could be due to > > > either the compiler or binutils) > > > -- Could not identify number of AVX-512 units - detection program > missing > > > compilation prerequisites > > > -- Could not run code to detect number of AVX-512 FMA units - > assuming 2. > > > -- Detected best SIMD instructions for this CPU - AVX_512 > > > CMake Error at cmake/gmxManageSimd.cmake:51 (message): > > > Cannot find AVX 512F compiler flag. Use a newer compiler, or > choose a > > > lower level of SIMD (slower). > > > Call Stack (most recent call first): > > > cmake/gmxManageSimd.cmake:186 > > > (gmx_give_fatal_error_when_simd_support_not_found) > > > CMakeLists.txt:719 (gmx_manage_simd) > > > > > > > > > Thanks, > > > Shlomit > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
Re: [gmx-users] Error: Cannot find AVX 512F compiler flag
That tells you what your CPU is capable of. We need to know whether cmake has found the compiler that can issue the instructions. Follow the suggestions Roland and I have made. Mark On Wed, 15 Jan 2020 at 10:45, Shlomit Afgin wrote: > > > I ran: > > cat /proc/cpuinfo | grep -i avx512 > > > > and got: > > avx512f avx512dq avx512cd avx512bw avx512vl > > > > So I thought I can use it. Am I wrong? > > > > Shlomit > > > > On 15/01/2020, 11:14, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Szilárd Páll" < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > pall.szil...@gmail.com> wrote: > > > > Hi, > > > > What hardware are you targeting? Unless you need AVX512 support, you > could > > just manually specify the appropriate setting in GMX_SIMD, e.g. > > -DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 > is not > > supported. > > > > Cheers, > > -- > > Szilárd > > > > > > On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin < > shlomit.af...@weizmann.ac.il> > > wrote: > > > > > > > > Hi, > > > I tried to install GROMACS 2019.5 on CentOS7, > > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > > > > > I have already installed devtoolset-6 and still get this error: > > > > > > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS > > > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed > > > -- Could not find any flag to build test source (this could be due to > > > either the compiler or binutils) > > > -- Could not identify number of AVX-512 units - detection program > missing > > > compilation prerequisites > > > -- Could not run code to detect number of AVX-512 FMA units - > assuming 2. > > > -- Detected best SIMD instructions for this CPU - AVX_512 > > > CMake Error at cmake/gmxManageSimd.cmake:51 (message): > > > Cannot find AVX 512F compiler flag. Use a newer compiler, or > choose a > > > lower level of SIMD (slower). > > > Call Stack (most recent call first): > > > cmake/gmxManageSimd.cmake:186 > > > (gmx_give_fatal_error_when_simd_support_not_found) > > > CMakeLists.txt:719 (gmx_manage_simd) > > > > > > > > > Thanks, > > > Shlomit > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: Cannot find AVX 512F compiler flag
How can I make GROMACS use devtoolset-6? [shlomit@cn gromacs-2019.5]$ type gcc gcc is /bin/gcc [shlomit@cn gromacs-2019.5]$ scl enable devtoolset-6 bash [shlomit@cn gromacs-2019.5]$ type gcc gcc is /bin/gcc Shlomit On 15/01/2020, 12:07, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Tru Huynh" wrote: On Wed, Jan 15, 2020 at 08:50:46AM +, Shlomit Afgin wrote: > > Hi, > I tried to install GROMACS 2019.5 on CentOS7, > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > I have already installed devtoolset-6 and still get this error: installed, but not using it? [tru@elitebook840g3 ~]$ type gcc gcc is /usr/bin/gcc [tru@elitebook840g3 ~]$ scl enable devtoolset-6 bash [tru@elitebook840g3 ~]$ type gcc gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc Tru -- Tru Huynh (PhD) | mailto:t...@pasteur.fr | tel +33 1 45 68 87 37 https://research.pasteur.fr/en/team/structural-bioinformatics/ Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: Cannot find AVX 512F compiler flag
On Wed, 15 Jan 2020 at 11:07, Tru Huynh wrote: > > gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc > Good, so is Cmake using it? (e.g. remove the build dir and run cmake again to see what it first reports, or inspect $builddir/CMakeCache.txt for the compiler setting) Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: Cannot find AVX 512F compiler flag
On Wed, Jan 15, 2020 at 08:50:46AM +, Shlomit Afgin wrote: > > Hi, > I tried to install GROMACS 2019.5 on CentOS7, > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > I have already installed devtoolset-6 and still get this error: installed, but not using it? [tru@elitebook840g3 ~]$ type gcc gcc is /usr/bin/gcc [tru@elitebook840g3 ~]$ scl enable devtoolset-6 bash [tru@elitebook840g3 ~]$ type gcc gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc Tru -- Tru Huynh (PhD) | mailto:t...@pasteur.fr | tel +33 1 45 68 87 37 https://research.pasteur.fr/en/team/structural-bioinformatics/ Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: Cannot find AVX 512F compiler flag
I ran: cat /proc/cpuinfo | grep -i avx512 and got: avx512f avx512dq avx512cd avx512bw avx512vl So I thought I can use it. Am I wrong? Shlomit On 15/01/2020, 11:14, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Szilárd Páll" wrote: Hi, What hardware are you targeting? Unless you need AVX512 support, you could just manually specify the appropriate setting in GMX_SIMD, e.g. -DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 is not supported. Cheers, -- Szilárd On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin wrote: > > Hi, > I tried to install GROMACS 2019.5 on CentOS7, > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > I have already installed devtoolset-6 and still get this error: > > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed > -- Could not find any flag to build test source (this could be due to > either the compiler or binutils) > -- Could not identify number of AVX-512 units - detection program missing > compilation prerequisites > -- Could not run code to detect number of AVX-512 FMA units - assuming 2. > -- Detected best SIMD instructions for this CPU - AVX_512 > CMake Error at cmake/gmxManageSimd.cmake:51 (message): > Cannot find AVX 512F compiler flag. Use a newer compiler, or choose a > lower level of SIMD (slower). > Call Stack (most recent call first): > cmake/gmxManageSimd.cmake:186 > (gmx_give_fatal_error_when_simd_support_not_found) > CMakeLists.txt:719 (gmx_manage_simd) > > > Thanks, > Shlomit > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: Cannot find AVX 512F compiler flag
Are you actually using the GCC from the devtoolset or the default one? Cmake tells you at the very beginning which compiler it is using. Roland > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se users-boun...@maillist.sys.kth.se> On Behalf Of Shlomit Afgin > Sent: Wednesday, January 15, 2020 12:51 AM > To: gmx-us...@gromacs.org > Subject: [gmx-users] Error: Cannot find AVX 512F compiler flag > > > Hi, > I tried to install GROMACS 2019.5 on CentOS7, cmake .. - > DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > I have already installed devtoolset-6 and still get this error: > > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed > -- Could not find any flag to build test source (this could be due to either > the > compiler or binutils) > -- Could not identify number of AVX-512 units - detection program missing > compilation prerequisites > -- Could not run code to detect number of AVX-512 FMA units - assuming 2. > -- Detected best SIMD instructions for this CPU - AVX_512 CMake Error at > cmake/gmxManageSimd.cmake:51 (message): > Cannot find AVX 512F compiler flag. Use a newer compiler, or choose a > lower level of SIMD (slower). > Call Stack (most recent call first): > cmake/gmxManageSimd.cmake:186 > (gmx_give_fatal_error_when_simd_support_not_found) > CMakeLists.txt:719 (gmx_manage_simd) > > > Thanks, > Shlomit > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: Cannot find AVX 512F compiler flag
Hi, What hardware are you targeting? Unless you need AVX512 support, you could just manually specify the appropriate setting in GMX_SIMD, e.g. -DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 is not supported. Cheers, -- Szilárd On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin wrote: > > Hi, > I tried to install GROMACS 2019.5 on CentOS7, > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > I have already installed devtoolset-6 and still get this error: > > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS > -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed > -- Could not find any flag to build test source (this could be due to > either the compiler or binutils) > -- Could not identify number of AVX-512 units - detection program missing > compilation prerequisites > -- Could not run code to detect number of AVX-512 FMA units - assuming 2. > -- Detected best SIMD instructions for this CPU - AVX_512 > CMake Error at cmake/gmxManageSimd.cmake:51 (message): > Cannot find AVX 512F compiler flag. Use a newer compiler, or choose a > lower level of SIMD (slower). > Call Stack (most recent call first): > cmake/gmxManageSimd.cmake:186 > (gmx_give_fatal_error_when_simd_support_not_found) > CMakeLists.txt:719 (gmx_manage_simd) > > > Thanks, > Shlomit > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error: Cannot find AVX 512F compiler flag
Hi, I tried to install GROMACS 2019.5 on CentOS7, cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON I have already installed devtoolset-6 and still get this error: -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed -- Could not find any flag to build test source (this could be due to either the compiler or binutils) -- Could not identify number of AVX-512 units - detection program missing compilation prerequisites -- Could not run code to detect number of AVX-512 FMA units - assuming 2. -- Detected best SIMD instructions for this CPU - AVX_512 CMake Error at cmake/gmxManageSimd.cmake:51 (message): Cannot find AVX 512F compiler flag. Use a newer compiler, or choose a lower level of SIMD (slower). Call Stack (most recent call first): cmake/gmxManageSimd.cmake:186 (gmx_give_fatal_error_when_simd_support_not_found) CMakeLists.txt:719 (gmx_manage_simd) Thanks, Shlomit -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
