Re: [gmx-users] GPU warnings

2012-12-09 Thread Thomas Evangelidis
gcc 4.7.2 is not supported by any CUDA version. I suggest that you just fix it by editing the include/host_config.h and changing the version check macro (line 82 AFAIK). I've never had real problems with using new and officially not supported gcc-s, the version check is more of a promise

[gmx-users] failed with intel compiler

2012-12-09 Thread Albert
Hello: I am compiling Gromacs4.6beta2 with intel cimpiler by command: cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/intel64/icc/bin/intel64/mpiCC -DCMAKE_C_COMPILER=/soft/intel64/icc/bin/intel64/icc But It fails with the following output: Change Dir:

[gmx-users] structure building and manipulating software

2012-12-09 Thread Amir Abbasi
Hi, I know that here for discussion about Gromacs,but I want to ask which program is the best for structure building and manipulating. I work on graphene and graphene oxide. best, Amir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

[gmx-users] amber to gromacs error

2012-12-09 Thread Albert
hello: I am using the command: acpype.py -p prmtop -x S13.rst to convert Amber system into Gromacs system, but it failed when I try to generate .tpr file: WARNING 1 [file prmtop_GMX.top, line 19]: Too few parameters on line (source file toppush.c, line 300) WARNING 2 [file

Re: [gmx-users] amber to gromacs error

2012-12-09 Thread Yun Shi
On Sun, Dec 9, 2012 at 9:46 AM, Albert mailmd2...@gmail.com wrote: hello: I am using the command: acpype.py -p prmtop -x S13.rst to convert Amber system into Gromacs system, but it failed when I try to generate .tpr file: WARNING 1 [file prmtop_GMX.top, line 19]: Too few parameters

Re: [gmx-users] failed with intel compiler

2012-12-09 Thread Roland Schulz
On Sun, Dec 9, 2012 at 11:30 AM, Albert mailmd2...@gmail.com wrote: Hello: I am compiling Gromacs4.6beta2 with intel cimpiler by command: cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/intel64/icc/bin/intel64/mpiCC -DCMAKE_C_COMPILER=/soft/intel64/icc/bin/intel64/icc You shouldn't

[gmx-users] Topolbuild configuration

2012-12-09 Thread SeokYun123
Hello! I'm trying to download topolbuild1_2_1 in my Mac computer. I understand that the executable file is in the same directory as the Makefile. I also understand the thing about the PATH. For different files I have downloaded, I was able to ./configure it and use make, but for topolbuild, I

[gmx-users] Error during compilation of Gromacs-4.5.5

2012-12-09 Thread BHARATI DUTTA
Hi, The following error pops up during compilation of Gromacs-4.5.5 : /home/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np'. Could you please help me fix it? I am installing it on uname -m = x86_64 uname -r = 2.6.9-5.ELsmp uname -s = Linux uname -v =

[gmx-users] GPU compatibility

2012-12-09 Thread Cara Kreck
Hi, We've got a GPU cluster in our group and have really been looking forward to running gromacs on it with full functionality. Unfortunately, it looks like our NVIDIA Tesla C1060 cards aren't supported by the 4.6 beta. I was just wondering if there was any chance that they would be