Re: [gmx-users] CygWin and Gromacs 4.5.5
On 13.11.2011 02:10, Mirco Wahab wrote: I was able to build Gromacs 4.5.5 (32 bit) on Cygwin (gcc 4.5.3) w/o threads For a better understanding of the usability of cygwin-compiled Gromacs under windows I performed some more tests on my desktop box. First, I tried to install recent versions of MPICH2 or OpenMPI in cygwin for creating a mdrun_mpi binary. Both MPI implementations won't compile under cygwin alone anymore (will require MSVC tools). Therefore, I tested the single-threaded mdrun version under cygwin. The result is compared with Gromacs compiled w/other toolchains on the same desktop machine. To compare architectures, runtime results on a cluster node (i7) are provided for the same simulated system. A. Simulated system -- 50nm Box w/coarse grained solvent (MARTINI W) and 10K coarse grained lipids (MARTINI DPPC), total number of particles ~ 1 Mio. No Ewald or PME, simple electrostatics w/shifted coulomb and rlist=1.3nm, large dt=0.04, v-rescale and isotropic Berendsen pcoupl. Large, but simple system. Gromacs 4.5.5 has been compiled from source as good as possible. The GFlops values have been copied from mdrun output ending after 2000 steps (or 200 steps for cygwin-mdrun). B. Box@Home: PhenomII/X6 3.4GHz, 4GB DDR3, Windows 7 Pro/x64 No GFlops System 1 | 11.3 | Win64 native (MSVC 2010 SP1 + SDK 7.1 SP1), 6 Threads, 3x2x1 2 | 11.1 | SuSE 12.1rc (GCC 4.6) as VMWare Guest OS, 6 Threads, 3x2x1 3 | 0.49 | CygWin 1.7.9-1/Setup 2.738 (GCC 4.5.3), Single Thread, no DD For the cygwin run, the mdrun.exe process has been allocated to one cpu core and its priority was set to 'high'. These optimizations didn't change the outcome at all. Maybe on a Win32 box (instead of Win64), the situation is different? C. For comparison: i7/2600K @4.2GHz, 4GB DDR3, SuSE 11.3/x64 No GFlops System 1 | 14.0 | GCC 4.5.1 (4 Threads, 4 x 1 x 1) 2 | 14.3 | ICC 12.0.4 (4 Threads, 4 x 1 x 1) 3 | 19.6 | GCC 4.5.1 (8 Threads, 4 x 2 x 1) 4 | 19.9 | ICC 12.0.4 (8 Threads, 4 x 2 x 1) Regards, M. -- gmx-users mailing listgmx-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
Re: [gmx-users] CygWin and Gromacs 4.5.5
On 10.11.2011 15:28, Szilárd Páll wrote: On Tue, Nov 8, 2011 at 11:59 PM, Mark Abrahammark.abra...@anu.edu.auwrote: Actually I don't think this issue has been addressed. Some NUMA-aware thread_mpi stuff does not work under Cygwin, and code added since 4.5.4 assumes that it does. I can find no reason to support that assumption. To work around, use configure --disable-threads. This seems to be correct for the current situation (CygWin 2.738 + Gromacs 4.5.5). I was able to build Gromacs 4.5.5 (32 bit) on Cygwin (gcc 4.5.3) w/o threads: $ tar xzf gromacs-4.5.5.tar.gz $ mkdir build; cd build $ LDFLAGS=-L/usr/local/lib/ -llapack -lblas -lgfortran \ ../gromacs-4.5.5/configure \ --disable-threads --with-fft=fftw3 --with-gsl --with-external-lapack --with-external-blas $ make install This worked *after* I compiled and installed fftw3: $ ./configure --with-our-malloc16 --enable-threads \ --enable-float --enable-sse $ make -j 4 and Lapack 3.3.1 from source on this cygwin installation (packaged version won't work due to missing s* linkage, as fas as I understood). Performance on the system I tested is rather poor. I used a membrane system w/10^6 Particles (Martini/NPT, coulombtype=Shift), the main memory used ~ 300MB. This has been tested on a PhenomII/X6 @3400MHz. (The same system is runnning also under Linux on a i7/2600K @4.2GHz) : 4.5.5/32b | Cygwin-version: 0.5 GFlops (single process only) 4.5.5/64b | Windows-version: ~10 GFlops (6 threads) 4.5.5/64b | Linux/icc: ~20GFlops (8 threads) I'd be surprised. Why should MSVC outperform gcc? That statement was based on my previous experience which, admittedly, might be outdated. I don't remember the exact details, but from what I recall, the I had to fiddle quite a lot with gcc optimizations to get the performance close to MSVC. One detail might be important: the code I was working on is C/C++ mix which quite a lot of ++ in it. Anyway, to get a better picture, it would be nice if people running GROMACS on Windows could share their experience/performance numbers. The Linux-compiled (both gcc and icc) versions *and* the native Windows-64 report after startup: ... Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. ... whereas, the Cygwin-compiled version says: ... Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present. ... So I don't have any idea why it would be that slow, (even scaled by 6 or processor affinity set) compared to the msvc-64 (2010) compiled version. There's enough memory and no disk activity during tests. Regards, M. -- gmx-users mailing listgmx-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
Re: [gmx-users] CygWin and Gromacs 4.5.5
yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I hope this issue will be addressed.Thanks From: Roland Schulz rol...@utk.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 9, 2011 11:03 AM Subject: Re: [gmx-users] CygWin and Gromacs 4.5.5 On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 8/11/2011 11:35 PM, Szilárd Páll wrote: Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? The file performance is horrible with cygwin (even much slower than a virtual machine). But this should only be important for analysis. For simulation I agree that the performance should be as good (I don't know about NUMA) . Roland Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 listgmx-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
Re: [gmx-users] CygWin and Gromacs 4.5.5
On Tue, Nov 8, 2011 at 11:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/11/2011 11:35 PM, Szilárd Páll wrote: Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Actually I don't think this issue has been addressed. Some NUMA-aware thread_mpi stuff does not work under Cygwin, and code added since 4.5.4 assumes that it does. I can find no reason to support that assumption. To work around, use configure --disable-threads. Some of that information might have not gone into the wiki (http://goo.gl/ALQuC) - especially that the page appears to be intact for the last 7 months. [Which is a pity and it would be really much appreciated if people in the future contribute back!!!] Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? That statement was based on my previous experience which, admittedly, might be outdated. I don't remember the exact details, but from what I recall, the I had to fiddle quite a lot with gcc optimizations to get the performance close to MSVC. One detail might be important: the code I was working on is C/C++ mix which quite a lot of ++ in it. Anyway, to get a better picture, it would be nice if people running GROMACS on Windows could share their experience/performance numbers. -- Szilárd Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/**thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/** 2009-September/044792.htmlhttp://cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] CygWin and Gromacs 4.5.5
On Thu, Nov 10, 2011 at 5:37 AM, Mr Bernard Ramos bgrquan...@yahoo.comwrote: yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I hope this issue will be addressed.Thanks The slow IO performance under cygwin is a known problem with the approach of cygwin and happens with any cygwin program and cannot be fixed by GROMACS. If you want decent IO performance you need to either use Visual C++ or Msys/MingW (see http://redmine.gromacs.org/issues/448). Roland -- *From:* Roland Schulz rol...@utk.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, November 9, 2011 11:03 AM *Subject:* Re: [gmx-users] CygWin and Gromacs 4.5.5 On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/11/2011 11:35 PM, Szilárd Páll wrote: Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? The file performance is horrible with cygwin (even much slower than a virtual machine). But this should only be important for analysis. For simulation I agree that the performance should be as good (I don't know about NUMA) . Roland Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing listgmx-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 listgmx-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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive
[gmx-users] CygWin and Gromacs 4.5.5
Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing listgmx-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
Re: [gmx-users] CygWin and Gromacs 4.5.5
Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Some of that information might have not gone into the wiki (http://goo.gl/ALQuC) - especially that the page appears to be intact for the last 7 months. [Which is a pity and it would be really much appreciated if people in the future contribute back!!!] Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM, bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- 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 listgmx-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
Re: [gmx-users] CygWin and Gromacs 4.5.5
I have read and have carried out the instruction on the given page. The error arises again. Igor В письме от Втр, 08 Ноя 2011, 16:35 Szilárd Páll пишет: Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Some of that information might have not gone into the wiki (http://goo.gl/ALQuC) - especially that the page appears to be intact for the last 7 months. [Which is a pity and it would be really much appreciated if people in the future contribute back!!!] Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM, bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- 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 listgmx-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 listgmx-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
Re: [gmx-users] CygWin and Gromacs 4.5.5
On 8/11/2011 11:35 PM, Szilárd Páll wrote: Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Actually I don't think this issue has been addressed. Some NUMA-aware thread_mpi stuff does not work under Cygwin, and code added since 4.5.4 assumes that it does. I can find no reason to support that assumption. To work around, use configure --disable-threads. Some of that information might have not gone into the wiki (http://goo.gl/ALQuC) - especially that the page appears to be intact for the last 7 months. [Which is a pity and it would be really much appreciated if people in the future contribute back!!!] Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] CygWin and Gromacs 4.5.5
On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/11/2011 11:35 PM, Szilárd Páll wrote: Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? The file performance is horrible with cygwin (even much slower than a virtual machine). But this should only be important for analysis. For simulation I agree that the performance should be as good (I don't know about NUMA) . Roland Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing listgmx-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 listgmx-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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-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
