Re: [gmx-users] Building gromacs on CRAY XC40
Hi, your not saying what version you are trying to install. Assuming 5.0.5 it should just work with cmake -DGMX_BUILD_SHARED_EXE=off .. Make sure to select GCC or ICC as compiler with a command such as (might be different on your machine) module swap PrgEnv-pgi PrgEnv-gnu If it still doesn't work, send your exact steps and errors. Roland On Tue, Jul 7, 2015 at 1:02 AM, Sabyasachi Sahoo ssahoo.i...@gmail.com wrote: Dear Gromacs users, I am trying to build gromacs on our latest supercomputer CRAY XC40, but I am unable to do so because of lack of administrator privileges and different programming environment, w.r.t. my previous experience on tyrone supercomputers. I continuously get errors regarding something or the other, but trying to solve that results in another error. I am sure many of you would have already build gromacs on cray machines, and hence would be really grateful, if anyone can tell me the correct sequence of steps to build gromacs. I have extensively searched through the web, and documentation and nothing seems to work. It be also really great if someone could give me the link to the any thread that addresses this problem. Thanx in advance. -- Yours sincerely, Sabyasachi Sahoo -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5
Hi, yes the variable is ignored. Because with GROMACS 5 large file support is required. Thus if the variable is set to false it also prints a fatal error. It was never a variable which was suppose to be set by the user. Why do you ask? What do you try to achieve? Roland On Tue, Jun 23, 2015 at 3:50 AM, Makoto Yoneya makoto-yon...@aist.go.jp wrote: Dear GROMACS users: I found that GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5 (e.g. cmake -DGMX_LARGEFILES=OFF bra-bra). At the end of cmake, it says CMake Warning: Manually-specified variables were not used by the project: GMX_LARGEFILES. Although, there are lines, include(gmxTestLargeFiles) gmx_test_large_files(GMX_LARGEFILES) in CMakeLists.txt file, this test looks skipped in actual cmake (no message on this test). Any info.s on this subject will be welcome! Regards, Makoto Yoneya, Dr. AIST, Tsukuba JAPAN -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] gromacs-5.0.4 installation problem
Hi, please rerun cmake from an empty build directly and post both the full cmake output and the content of CMakeFiles/CMakeError.log. Roland On Thu, May 7, 2015 at 7:38 PM, James Lord jjamesgreen...@gmail.com wrote: Hi Mark,Szilard and Christopher, Thanks for the comments, apparently gcc 4.8.2 is there. Really can't understand why and what it is complaining about, root@ubuntu:~/gromacs-5.0.4/build# gcc --version gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. So are you guys saying that a new installation might be better than messing around with this? Cheers James On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll pall.szil...@gmail.com wrote: Something is strange about that Ubuntu installation, gcc 4.8.2 should be the default. -- Szilárd On Fri, May 8, 2015 at 12:10 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The error means you need a newer compiler in order to take advantage of your hardware, e.g. the latest version of gcc you can get (which will probably require you add a new PPA), though I am surprised that cmake found a C++ compiler on 14.04 and then didn't find AVX support in it... something seems strange. Mark On Thu, May 7, 2015 at 8:46 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? Cheers James -- 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. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL
Re: [gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed
On Tue, Dec 16, 2014 at 10:09 AM, Mike Hanby mha...@uab.edu wrote: Howdy, I'm attempting to build Gromacs 5.0.4 using Intel compilers 13.1.1 for one of the users of our HPC fabric and it errors when running test 13 during the make check There are several known problems with ICC 13. This might be one of it. Please use at least ICC 14. Roland [--] Global test environment tear-down [==] 139 tests from 8 test cases ran. (462 ms total) [ PASSED ] 138 tests. [ FAILED ] 1 test, listed below: [ FAILED ] SelectionCollectionDataTest.HandlesCharge 1 FAILED TEST Total Test time (real) = 148.29 sec The following tests FAILED: 13 - SelectionUnitTests (Failed) Errors while running CTest make[3]: *** [CMakeFiles/run-ctest] Error 8 make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2 make[1]: *** [CMakeFiles/check.dir/rule] Error 2 make: *** [check] Error 2 I've attached the cmake, make and make check logs. Any suggestions on what I can do to debug / fix this issue, or is it benign and I can safely move on to installing? Thanks, Mike -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] avx2 with gcc 4.8.3
Hi, CMakeFiles/CMakeError.log should show why cmake thinks your gcc doesn't support -mavx2. Roland On Mon, Dec 15, 2014 at 9:18 AM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear Mark, Here is where it fails: -- Try C++ compiler AVX2 flag = [-mavx2] -- Performing Test CXX_FLAG_mavx2 -- Performing Test CXX_FLAG_mavx2 - Success -- Performing Test CXX_SIMD_COMPILES_FLAG_mavx2 -- Performing Test CXX_SIMD_COMPILES_FLAG_mavx2 - Failed -- Try C++ compiler AVX2 flag = [/arch:AVX] -- Performing Test CXX_FLAG_arch_AVX -- Performing Test CXX_FLAG_arch_AVX - Failed -- Try C++ compiler AVX2 flag = [-hgnu] -- Performing Test CXX_FLAG_hgnu -- Performing Test CXX_FLAG_hgnu - Failed -- Try C++ compiler AVX2 flag = [] -- Performing Test CXX_FLAG_ -- Performing Test CXX_FLAG_ - Success -- Performing Test CXX_SIMD_COMPILES_FLAG_ -- Performing Test CXX_SIMD_COMPILES_FLAG_ - Failed CMake Error at cmake/gmxTestSimd.cmake:244 (message): Cannot find AVX2 compiler flag. Use a newer compiler, or choose AVX SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) Well, which ones fail? Inspecting the compiler output (e.g. using cmake --debug-trycompile and poking around it its output) is probably the only way to find that problem. Mark - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel harry.greenbl...@weizmann.ac.ilmailto:harry.greenbl...@weizmann.ac.il -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] pseudo-random algorithm
Hi, Gromacs 5.0 uses a Mersenne twister. See gmx_random.h. Starting with 5.0 it uses Random123 threefry2x64. Why do you think your results are affected by the PRNG? Roland On Wed, Oct 29, 2014 at 6:23 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Before I start to feel optimistic about my alanine tripeptide simulation, can I know which pseudo-random number algorithm does my installation of gromacs 4.6.6 use? It was installed on linux centos 5 with kernel 2.6.32-220.7.1.el6.x86_64, and the machine has 12 intel cpu and no gpu. I was using the V-rescale thermostat. Thanks again. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Gromacs 5.0.2 installation on Stampede
Hi, assuming you want to run on the CPU, nothing special should be required. Make sure to let support know that they don't have the most recent version and they should install the most recent version. Roland On Wed, Oct 22, 2014 at 5:24 AM, Amrash agya...@gmail.com wrote: Dear all, I was wondering if there are any tricks needed to install Gromacs 5.0.2 on the Stampede supercomputer. I will be grateful, if you could share your experience and/or modifications needed to configuration files. Thanks, Amrash -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Issue building 5.0.2 release for GPU
Hi,
this seems to be the boost bug https://svn.boost.org/trac/boost/ticket/10420
. Please file a Gromacs redmine issue. As a temporary solution use
gcc=4.7. It should be as fast as ICC at least when used with GPU.
Roland
On Fri, Oct 17, 2014 at 2:23 AM, Éric Germaneau german...@sjtu.edu.cn
wrote:
Dear all,
I'm building the 5.0.2 release the same way as the 4.6.x releases but
can't compile it for GPU.
I use CUDA 6.5 and icc/14.0.2 and impi/4.1.3.048.
Here is my cmake command:
CC=mpiicc CXX=mpiicpc
CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin
\
$CMAKE \
-DFFTW_INCLUDE_DIR=$FFTW3DIR/include \
-DFFTW_LIBRARY=$FFTW3DIR/lib\
-DGMX_MPI=ON \
-DGMX_GPU=ON [-DCUDA_TOOLKIT_ROOT_DIR=$CUDAPATH] \
-DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
-DGMX_X11=OFF ../$APP \
-DGMX_THREADS=OFF \
-DBUILD_SHARED_LIBS=OFF \
-DGMX_PREFER_STATIC_LIBS=ON
Here is the kind of errors I get:
/tmp/tmpxft_88e3_-9_copyrite_gpu.compute_20.cudafe1.stub.c(6):
remark #82: storage class is not first
static void __nv_cudaEntityRegisterCallback(void **__T20){{
volatile static void * *__ref __attribute__((unused)); __ref =
(volatile void * *)__T20;
};__nv_save_fatbinhandle_for_managed_rt(__T20);}
^
In file included from
/path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/config.hpp(35),
from
/path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/smart_ptr/scoped_ptr.hpp(14),
from
/path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/scoped_ptr.hpp(14),
from
/path/to/gromacs/gromacs-5.0.2/src/gromacs/utility/common.h(50),
from
/path/to/gromacs/gromacs-5.0.2/src/gromacs/mdlib/nbnxn_cuda/
nbnxn_cuda_data_mgmt.cu(63):
/path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/config/compiler/intel.hpp(40):
warning #47: incompatible redefinition of macro BOOST_COMPILER
(declared at line 11 of
/path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/config/compiler/nvcc.hpp)
#define BOOST_COMPILER Intel C++ version
BOOST_STRINGIZE(BOOST_INTEL_CXX_VERSION)
^
Do I have to install Boost?
I actually just tried but it's horrible with Intel MPI.
Any suggestions?
Thanks,
Éric.
--
Éric Germaneau (艾海克), Specialist
Center for High Performance Computing
Shanghai Jiao Tong University
Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
M:german...@sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn
--
Gromacs Users mailing list
* Please search the archive at
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send a mail to gmx-users-requ...@gromacs.org.
--
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865-241-1537, ORNL PO BOX 2008 MS6309
--
Gromacs Users mailing list
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Re: [gmx-users] [gmx-developers] About dynamics loading balance
Hi, On Thu, Aug 21, 2014 at 1:56 PM, Yunlong Liu yliu...@jh.edu wrote: Hi Roland, The problem I am posting is caused by trivial errors (like not enough memory) and I think it should be a real bug inside the gromacs-GPU support code. It is unlikely a trivial error because otherwise someone else would have noticed. You could try the release-5-0 branch from git, but I'm not aware of any bugfixes related to memory allocation. The memory allocation which causes the error isn't the problem. The printed size is reasonable. You could recompile with PRINT_ALLOC_KB (add -DPRINT_ALLOC_KB to CMAKE_C_FLAGS) and rerun the simulation. It might tell you where the usual large memory allocation happens. PS: Please don't reply to an individual Gromacs developer. Keep all conversation on the gmx-users list. Roland That is the reason why I post this problem to the developer mailing-list. My system contains ~240,000 atoms. It is a rather big protein. The memory information of the node is : top - 12:46:59 up 15 days, 22:18, 1 user, load average: 1.13, 6.27, 11.28 Tasks: 510 total, 2 running, 508 sleeping, 0 stopped, 0 zombie Cpu(s): 6.3%us, 0.0%sy, 0.0%ni, 93.7%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 32815324k total, 4983916k used, 27831408k free, 7984k buffers Swap: 4194296k total,0k used, 4194296k free, 700588k cached I am running the simulation on 2 nodes, 4 MPI ranks and each rank with 8 OPENMP-threads. I list the information of their CPU and GPU here: c442-702.stampede(1)$ nvidia-smi Thu Aug 21 12:46:17 2014 +--+ | NVIDIA-SMI 331.67 Driver Version: 331.67 | |---+--+--+ | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 Tesla K20m Off | :03:00.0 Off |0 | | N/A 22CP046W / 225W |172MiB / 4799MiB | 0% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0113588 /work/03002/yliu120/gromacs-5/bin/mdrun_mpi 77MiB | |0113589 /work/03002/yliu120/gromacs-5/bin/mdrun_mpi 77MiB | +-+ c442-702.stampede(4)$ lscpu Architecture: x86_64 CPU op-mode(s):32-bit, 64-bit Byte Order:Little Endian CPU(s):16 On-line CPU(s) list: 0-15 Thread(s) per core:1 Core(s) per socket:8 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family:6 Model: 45 Stepping: 7 CPU MHz: 2701.000 BogoMIPS: 5399.22 Virtualization:VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 20480K NUMA node0 CPU(s): 0-7 NUMA node1 CPU(s): 8-15 I hope this information will help. Thank you. Yunlong On 8/21/14, 1:38 PM, Roland Schulz wrote: Hi, please don't use gmx-developers for user questions. Feel free to use it if you want to fix the problem, and have questions about implementation details. Please provide more details: How large is your system? How much memory does a node have? On how many nodes do you try to run? How many mpi-ranks do you have per node? Roland On Thu, Aug 21, 2014 at 12:21 PM, Yunlong Liu yliu...@jh.edu wrote: Hi Gromacs Developers, I found something about the dynamic loading balance really interesting. I am running my simulation on Stampede supercomputer, which has nodes with 16-physical core ( really 16 Intel Xeon cores on one node ) and an NVIDIA Tesla K20m GPU associated. When I am using only the CPUs, I turned on dynamic loading balance by -dlb yes. And it seems to work really good, and the loading imbalance is only 1~2%. This really helps improve the performance by 5~7%。But when I am running my code on GPU-CPU hybrid ( GPU node, 16-cpu and 1 GPU), the dynamic loading balance kicked in since the imbalance goes up to ~50% instantly after loading. Then the the system reports a fail-to-allocate-memory error: NOTE: Turning on dynamic load balancing --- Program mdrun_mpi, VERSION 5.0 Source code file: /home1/03002/yliu120/build/gromacs-5.0/src/gromacs/utility/smalloc.c, line: 226 Fatal error: Not enough memory. Failed to realloc
Re: [gmx-users] Installing 5.0 on Cygwin - Getting error
Hi, you either need to use this patch: https://gerrit.gromacs.org/#/c/3764, or the latest release-5-0 branch (which includes the patch), or add -std=gnu++0x to the CXXFLAGS. Roland On Mon, Jul 21, 2014 at 6:51 PM, John Doe helstr...@hotmail.com wrote: Hello, I'm attempting to install Gromacs-5.0 on Cygwin64. I have a full install of Cygwin and I'm following the Quick and dirty installation instructions. In the make step, I am getting the following error and have no clue what it means. Any help would be great. [ 8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.c.o /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/topshake.c: In function ‘count_hydrogens’: /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/topshake.c:98:9: warning: array subscript has type ‘char’ [-Wchar-subscripts] if (toupper(**(atomname[a[i]])) == 'H') ^ /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/topshake.c: In function ‘make_shake’: /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/topshake.c:165:37: warning: array subscript has type ‘char’ [-Wchar-subscripts] (numhydrogens == 1 toupper(**(info[ang-a[1]])) == 'O')) ^ [ 8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.c.o [ 8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.c.o [ 8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.c.o [ 8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.c.o [ 8%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp: In function ‘int low_fflib_search_file_end(const char*, gmx_bool, const char*, gmx_bool, char***, char***)’: /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp:205:47: error: ‘strdup’ was not declared in this scope fns[n] = strdup(fn_dir); ^ /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp: In function ‘int fflib_search_file_in_dirend(const char*, const char*, char***)’: /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp:298:47: error: ‘strdup’ was not declared in this scope dns[n] = strdup(f_short[i]); ^ src/gromacs/CMakeFiles/libgromacs.dir/build.make:1391: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o' failed make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o] Error 1 CMakeFiles/Makefile2:1924: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 Makefile:146: recipe for target 'all' failed make: *** [all] Error 2 -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Installing 5.0 on Cygwin - Getting error
On Mon, Jul 21, 2014 at 7:17 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 22.07.2014 00:51, John Doe wrote: [ 8%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp: In function ‘int low_fflib_search_file_end(const char*, gmx_bool, const char*, gmx_bool, char***, char***)’: /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp:205:47: error: ‘strdup’ was not declared in this scope fns[n] = strdup(fn_dir); clean up the build directory, + add -DBUILD_SHARED_LIBS=off to your cmake invocation why? For me it works fine without. What problem do you see without this? If this is something common we probably should set this by default. + edit gromacs file src/external/thread_mpi/src/impl.h add (as first line) above everything else: #define HAVE_SYS_TIME_H in which cases do you need to do that? If we can identify the problem we can fix it in cmake. Roland + rebuild Regards M. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Git Gromacs Cygwin Build - Error
On Mon, Jul 21, 2014 at 9:48 PM, John Doe helstr...@hotmail.com wrote: Attempting to build the Git clone (git clone https://gerrit.gromacs.org/gromacs) In general if you are a user and not a developer you want to use the latest release branch (contains only bugfixes relative since the last version) and not the master branch (might contain unstable development). For that you want to use git clone -b release-5-0 https://gerrit.gromacs.org/gromacs; or if you have it already cloned git checkout release-5-0. with full Cygwin and following the Quick and dirty installation instructions, but I'm getting the following error: -- [ 91%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o make[2]: *** No rule to make target '//home/User/gromacs/build/src/contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a', needed by 'bin/cyggromacs-1.dll'. Stop. CMakeFiles/Makefile2:2000: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 Makefile:146: recipe for target 'all' failed make: *** [all] Error 2 --- I just uploaded a patch for this: https://gerrit.gromacs.org/#/c/3813/2 You can either use the patch or don't use GMX_BUILD_OWN_FFTW. Cygwin comes with fftw. Roland Thanks for the help -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Problems in compiling GROMACS with VMD plugin
Hi, GMX_USE_PLUGINS has to be enabled in your CMackeCache.txt. Are you building under Linux? It probably didn't find dlopen support. Look for Result of test for dlopen when you run cmake in a new build folder. You can see in CMakeFiles/CMakeError.log why the dlopen test fails. Roland On Tue, Jul 8, 2014 at 10:27 AM, ming ma morning22...@gmail.com wrote: Hi, I met some problems in compiling GROMACS with VMD plugin. Generally speaking, the compilation is finished, but it did't involve vmd plugin. I first complied the serial version of GROMACS, the VMDDIR is set as export VMDDIR=/home/ming/lib/vmd191 where vmd is installed, [ming@mingtlv vmd191]$ pwd /home/ming/lib/vmd191 [ming@mingtlv vmd191]$ ls Announcementlibexpat.so.0plugins shaders tachyon_LINUXAMD64 doc libsqlite3.so.0 README stride_LINUXAMD64 vmd_completion.dat libcudart.so.4 LICENSE scripts surf_LINUXAMD64vmd_LINUXAMD64 , then I complied GROMACS successfully. Then I set the VMD_PLUGIN_PATH [ming@mingtlv g-van]$ echo $VMD_PLUGIN_PATH /home/ming/lib/vmd191/plugins/LINUXAMD64/molfile however, when I trying to use g_vanhove to load a LAMMPS trajectory with g_vanhove -f ../traj.lammpstrj -s topol.tpr -om vanhove.xpm -rmax 20 -rbin 0.1 I met the following problem, Program g_vanhove, VERSION 4.6.5 Source code file: /home/ming/software/gromacs-4.6.5/src/gmxlib/trxio.c, line: 1040 Fatal error: Not supported in read_first_frame: ../traj.lammpstrj. Please make sure that the file is a trajectory. GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins. Please compile with plug-in support if you want to read non-GROMACS trajectory formats. So it seems that GROMACS was not compiled with the vmd plugin. For example, in the compiling_directory/src/config.h, I can't find GMX_DLOPEN, and in the output of the compilation, by searching for vmd and VMD, I can only find lines [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o Sorry anybody have ideas how I can solve this problem? Best Ming -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Gromacs 5.0 download
Maybe something on your end is blocking ftp connections. You can download from a mirror such as: http://fossies.org/linux/privat/gromacs-5.0.tar.gz If you download from a mirror make sure to check the md5sum. On Wed, Jul 2, 2014 at 4:36 PM, Szilárd Páll pall.szil...@gmail.com wrote: The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Gromacs 5.0 download
On Wed, Jul 2, 2014 at 6:55 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I ran the md5sum but it does not match with any of the hashes.What should I do now? Which file from which server (/which URL) did you download? What md5 did you get? Roland On Wed, Jul 2, 2014 at 5:55 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 4:36 PM, Szilárd Páll wrote: The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s I'm having a similar problem as the OP. The web interface just seems to hang and using wget takes over an hour with a download rate of 4 KB/sec. This is true at work (hardwired workstation) and at home (laptop on wifi) OK, that's alarming. Perhaps uu.se (which hosts ftp.gromacs.org) got hit hard by the downloads and they throttle (some) connections. Note mine, though, as you can see I got a 28.6 M/s average download speed (but that's of course an unfair comparison). Not sure how to check whether the downloads are really being throttled, but perhaps we should use an alternative host or torrent. -Justin 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Compilation issues with GROMACS 5 beta 2
Hi
we have fixed quite a few installation issues since beta2. Could you try to
download the latest version from git?
git clone git://git.gromacs.org/gromacs.git
Let us know if you still see the issue.
If you don't have git you can download it from:
https://github.com/gromacs/gromacs/archive/master.zip
Roland
On Mon, Mar 17, 2014 at 8:10 AM, jk broodkil...@gmail.com wrote:
Hello everyone, my name is Jacek and I am new to GROMACS :) I have recently
downloaded and tried to compile the second beta of GROMACS 5, and run into
some issues along the way, so I decided to ask around and see if I can find
some help. Basically, what I wanted to do was to compile a few different
variants of GROMACS 5 to see how they perform against each other. I was
interested in comparing single and double precision builds, CUDA vs no CUDA
and MPI vs no MPI, in various combinations. Eventually though, I have only
managed to succesfully compile a single-precision, CUDA-extended and
MPI-paralellized build, and none other.
Now to the details:
(1) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=OFF
terminates early with a fatal error of lacking MPI headers:
[ 3%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o
In file included from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/commrec.h:40:0,
from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/coulomb.h:43,
from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/gmxpreprocess/calc_verletbuf.c:49:
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/../../utility/gmxmpi.h:62:17:
fatal error: mpi.h: No such file or directory
compilation terminated.
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o]
Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2
(2) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=ON
terminates exactly the same, but after some CUDA stuff is compiled.
(3) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=ON and -DGMX_GPU=OFF
terminates at link with a fatal error of lacking CUDA-specific objects:
[ 92%] Building CXX object
share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs_mpi.so.0.0.0: undefined reference to
`nbnxn_cuda_init_const'
(...some more undefined refs)
../../lib/libgromacs_mpi.so.0.0.0: undefined reference to
`pick_compatible_gpus'
collect2: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2
(4) Compiling with -DGMX_DOUBLE=OFF, -DGMX_GPU=ON and -DGMX_MPI=ON works
fine, as mentioned before.
(5) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=OFF and -DGMX_GPU=OFF
terminates identically as (1)
(6) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=ON and -DGMX_GPU=OFF
terminates identically as (3)
Each recompilation attempt was made in a fresh direction, with all the
files
from a previous build removed, so as to avoid any conflicts. I can post
links to complete compilation logs to PasteBin, if necessary. On the
technical side of things, I am running a 64-bit Ubuntu 12.04 system on a
quad-core i7-860 CPU, with 16GB of RAM and a brand new GTX 780Ti gfx card
on
hand-compiled CUDA 5.5 (driver+toolkit).
Of the relevant libs, I have the latest FFTW-3.3.3 compiled nicely in
single
('--enable-float --enable-shared --enable-sse2') and double precision
('--enable-shared --enable-sse2') variants stored in separate folders,
which
I pass to Cmake through the -DFFTW(F)_LIBRARY parameter. I have OpenMPI
1.4.3.2, MPICH2 and libboost 1.46.1, all from the offical Ubuntu repo.
My guess is that the build system somehow disregards the flags sent to it
and wants MPI/CUDA files even when directly told to skip them. Any ideas on
how to fix/work around this?
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Re: [gmx-users] GROMACS 5.0 - second beta released!
Hi, I uploaded fixes for both issues: https://gerrit.gromacs.org/#/c/3040/ https://gerrit.gromacs.org/#/c/3041/ Thanks for the feedback. Roland On Wed, Jan 29, 2014 at 12:59 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 29.01.2014 15:06, Mirco Wahab wrote: A test run (martini small vesicle system, 250K atoms) did start promising but crashed after 15 min without any indication. (I'll try without gpu later). I identified the problem. It is the same problem that also required a patch in the 4.6.x versions on Windows. The default stack size with Visual Studio compilers is 1MB, therefore you have to modify: - - - - - - - - - - - - - - - - - - - - - - - - - - - ../gromacs-5.0-beta2/src/gromacs/fileio/gmxfio.c [gmxfio.c] l 680: #define CPT_CHK_LEN 1048576 md5_state_t state; unsigned char buf[CPT_CHK_LEN]; change last line to: static unsigned char buf[CPT_CHK_LEN]; - - - - - - - - - - - - - - - - - - - - - - - - - - - after this, builds and runs work perfectly. M. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Compilation issue with F77_FUNC functions?
Hi, what compiler is used by mpicc? What does mpicc -showme and mpicc --version show? Does it help to uncomment the line containing F77_FUNC int src/config.h.cmakein? Roland On Sun, Dec 8, 2013 at 7:44 PM, Michael Shirts mrshi...@gmail.com wrote: So, I'm trying to compile with MPI using mpich3. Previous installations worked, and installations without MPI worked. I'm getting errors like: /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: warning: parameter names (without types) in function declaration /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: error: function ‘F77_FUNC’ is initialized like a variable /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: braces around scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: invalid initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) And it keeps on like that for a long while. Any suggestions? Perhaps something wrong in the way mpicc is handling Fortran code? -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Virtual Sites
Hi, I haven't tried it but it should work if you set verlet-buffer-drift=-1 and set rlist manually. Roland On Mon, Dec 2, 2013 at 3:20 PM, Brad Van Oosten bv0...@brocku.ca wrote: I am trying to add virtual sites to a simulation with no mass or charge, just to make tracking the center of mass of groups later easier later on. However, I keep getting the warning The mass of a vsiten constructing atom is = 0 when i run grompp. Here's the section of my .itp file where i have defined them: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 CHX rtp CHX q 0.0 1 CLAL 1CHXCL1 1 -0.151 35.453 ; qtot -0.151 . . . . 63 CA 1CHXCZ2 63 0.083 12.011 ; qtot 0.144 64 CLAL 1CHXCL2 64 -0.144 35.453 ; qtot 0 65 MCH3 1CHX V1 65 0 0 ; 66 MCH3 1CHX V2 66 0 0 ; 67 MCH3 1CHX V3 67 0 0 ; 68 MCH3 1CHX V4 68 0 0 ; 69 MCH3 1CHX V5 69 0 0 ; 70 MCH3 1CHX V6 70 0 0 ; 71 MCH3 1CHX V7 71 0 0 ; 72 MCH3 1CHX V8 72 0 0 ; 73 MCH3 1CHX V9 73 0 0 ; 74 MCH3 1CHXV10 74 0 0 ; 75 MCH3 1CHXV11 75 0 0 ; 76 MCH3 1CHXV12 76 0 0 ; [virtual_sitesn] 65 2 8 9 10 11 66 2 2 3 6 7 67 2 1 4 5 12 13 68 2 14 15 16 17 18 69 2 19 20 21 22 23 70 2 24 25 26 27 28 29 30 31 32 71 2 33 34 35 36 37 38 39 40 41 72 2 49 50 51 52 53 73 2 44 45 46 47 48 74 2 42 43 54 57 58 75 2 55 56 59 60 76 2 61 62 63 64 Am I defining something wrong here? -- View this message in context: http://gromacs.5086.x6.nabble.com/Virtual-Sites-tp5012975.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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.
