Re: [gmx-users] gromacs installation (2020&2019)

2 5275 > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Netaly > > Khazanov > > Sent: Sunday, April 26, 2020 15:38 > > To: Discussion list

Re: [gmx-users] gromacs installation (2020&2019)

_ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Netaly > Khazanov > Sent: Sunday, April 26, 2020 15:38 > To: Discussion list for GROMACS users > Subject: [gmx-users] gromacs installati

Re: [gmx-users] gromacs installation (2020&2019)

: [gmx-users] gromacs installation (2020&2019) Dear All, I am trying to install gromacs 2020 and 2019 versions on CentOS release 6.10 (Final) linux system. I passed throuht cmake compilation. Using command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX

[gmx-users] gromacs installation (2020&2019)

Dear All, I am trying to install gromacs 2020 and 2019 versions on CentOS release 6.10 (Final) linux system. I passed throuht cmake compilation. Using command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=gromacs2020

Re: [gmx-users] Gromacs installation to do coupled QMMM with Gaussian (Maryam Kowsar)

Hi, You need to compile with the QMMM-flag on GMX_QMMM_PROGRAM = gaussian of for older versions --with-qmmm-gaussian After that you can use the script at to run a QM/MM simulations with any version of the Gaussian program. http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian Best, Gerrit

[gmx-users] Gromacs installation to do coupled QMMM with Gaussian

Dear all, How can I compile Gromacs for doing QMM/MM computations with Gaussian ? Is there a special flag during installation process? I have read the instructions in http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM But it is not a step by step instruction. Your help

Re: [gmx-users] GROMACS Installation error on domdec.cpp

What version of MPI do you have? It may be helpful to indicate exact location of MPI if the paths are not automatically found. On 08/03/2018 02:43 PM, 郭聪 wrote: Hi All, I wanted to build GROMACS-2016.4 on hpc clusters but I got error with domdec.cpp. Could anyone helps me with that?

[gmx-users] GROMACS Installation error on domdec.cpp

Hi All, I wanted to build GROMACS-2016.4 on hpc clusters but I got error with domdec.cpp. Could anyone helps me with that? Thanks! ps: I succeeded to build it on my lab pc. I am wondering if something is wrong with GROMACS code or the compiler. I used gnu and openmpi. tar -zxvf

Re: [gmx-users] Gromacs installation with GPU support in Windows 7

:28 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Gromacs installation with GPU support in Windows 7 Hi, I've implemented the fix and I verified that it works on the command line; I've successfully complied the nvcc depend file. Nonetheless, CMake still fails on compiling in that stage

Re: [gmx-users] Gromacs installation with GPU support in Windows 7

, Harry From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Aleksei Iupinov Sent: Tuesday, May 22, 2018 4:59 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Gromacs installation with GPU support in Windows 7 Hello Harry, Thank you

Re: [gmx-users] Gromacs installation with GPU support in Windows 7

Hello Harry, Thank you for the report. It seems to be a trivial error in the code, indeed. It was not caught by the Gromacs automated testing since we don't have Windows + CUDA configuration in it. I have filed a bug report https://redmine.gromacs.org/issues/2509 and this will be fixed in Gromacs

[gmx-users] Gromacs installation with GPU support in Windows 7

Aim: Install Gromacs with GPU support in windows 7 Problem: Build step failed in Visual Studio 14 2015, using CMake 3.11 GUI in Windows Identified "issues": 1. First off, NVIDIA named their default CUDA installation directory in a space separated directory. This caused much grief when

Re: [gmx-users] gromacs installation

On Thu, Sep 7, 2017 at 3:25 PM, vijayakumar gosu wrote: > Hi, > > I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus. > I am allotted to use only 2 nodes with 80 cpus. after installation when i > did sample md run only 20 cpus are being

[gmx-users] gromacs installation

Hi, I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus. I am allotted to use only 2 nodes with 80 cpus. after installation when i did sample md run only 20 cpus are being utilized. How can I fully utilize the all 80 CPUs for mdrun. I have used below cmake command for the

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Good that it worked out. You might have changes something in your environment (path?) perhaps between last time and now. On Fri, Jul 7, 2017 at 10:57 PM, Seyed Mostafa Razavi wrote: > Strangely enough, I could install this time,and I do not know why. I > followed exact

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Strangely enough, I could install this time,and I do not know why. I followed exact same procedure except running make VERBOSE=1 Btw, here is the libgromacs_LIB_DEPENDS line in CMakeCache.txt if you want to know: libgromacs_LIB_DEPENDS:STATIC=general;/usr/lib64/libz.so;gen

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Strange. That means the GROAMCS build system somehow does not get the final link command right. Without investigating deeper, I'm not sure what would be the solution. I'd look a the actual link command that fails (make VERBOSE=1) and try to see what and why is missing. BTW, cmake should know

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Here is what I did: $ gcc -o omp_helloc -fopenmp omp_hello.c $ ./omp_helloc Hello World from thread = 0 Number of threads = 4 Hello World from thread = 3 Hello World from thread = 1 Hello World from thread = 2 Thank you, S. Mostafa Razavi On Fri, Jul 7, 2017 at 9:12 AM, Szilárd Páll

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Hi, That looks weird. Can you compile a sample OpenMP code, e.g. this https://computing.llnl.gov/tutorials/openMP/samples/C/omp_hello.c -- Szilárd On Fri, Jul 7, 2017 at 11:59 AM, Seyed Mostafa Razavi wrote: > Hello, > > I'm trying to install Gromacs (gromacs-2016.3) on

[gmx-users] Gromacs installation fails in CentOS 6.5

Hello, I'm trying to install Gromacs (gromacs-2016.3) on my CentOS 6.5 system. I exactly follow the installation instruction in http://manual.gromacs.org/ documentation/2016.3/install-guide/index.html. After I run "make", the installation process starts and proceeds to %97, then it gives me an

Re: [gmx-users] Gromacs installation on GPU

Hi, The more simple way to cater for all possibilities is to configure with GPU support the first time. mdrun observes whether there are actually GPUs at run time and executes accordingly. But as Justin says, this requires that you install CUDA when you might not use it, which is usually more

Re: [gmx-users] Gromacs installation on GPU

On 3/15/17 8:43 AM, Andrew Bostick wrote: Dear Gromacs users, I had installed gromacs using following commands: tar xvf cmake-3.6.1.tar.gz tar xvzf gromacs-5.1.3.tar.gz cd ../cmake-3.6.1. ./configure make make install cd ../gromacs-5.1.3 mkdir build cd build cmake ..

[gmx-users] Gromacs installation on GPU

Dear Gromacs users, I had installed gromacs using following commands: tar xvf cmake-3.6.1.tar.gz tar xvzf gromacs-5.1.3.tar.gz cd ../cmake-3.6.1. ./configure make make install cd ../gromacs-5.1.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON

Re: [gmx-users] Gromacs installation on GPU

http://manual.gromacs.org/documentation/2016/install-guide/index.html#cuda-gpu-acceleration -- Szilárd On Wed, Aug 10, 2016 at 11:47 AM, Atila Petrosian wrote: > *Dear* *Szilárd, * > > *Thanks for your answer,* > >> There's the issue. You need to tell the build > >>

[gmx-users] Gromacs installation on GPU

*Dear* *Szilárd, * *Thanks for your answer,* > There's the issue. You need to tell the build > system where CUDA is, e.g. by setting the > CUDA_TOOLKIT_ROOT_DIR environment variable. *How? Which command is required in linux?* *Best, * *Atila* -- Gromacs Users mailing list * Please search

Re: [gmx-users] Gromacs installation on GPU

On Tue, Aug 9, 2016 at 2:06 PM, Atila Petrosian wrote: > Dear gromacs users, > > I am installing gromacs in my system. My computational system is Rocks > 6.1.1. > > I encountered with following: > > [root@me build]# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON

Re: [gmx-users] Gromacs installation on GPU

Dear Atila, You need to install CUDA toolkit to access the GPU facility .you can get it from here https://developer.nvidia.com/cuda-toolkit GeForce GTX 480 Is an old card,i dont know how much you can achieve using this . -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Gromacs installation on GPU

Dear gromacs users, I am installing gromacs in my system. My computational system is Rocks 6.1.1. I encountered with following: [root@me build]# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_GPU=ON -- The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU

Re: [gmx-users] gromacs installation

but my folder which contains downloaded gromacs-5.1 and cmake and fftw are within other address On Mon, Jul 4, 2016 at 11:32 PM, roshanak starlight wrote: > when i was installing , i typed this: 'source > /usr/local/gromacs/bin/GMXRC' after 'sudo make install'

Re: [gmx-users] gromacs installation

when i was installing , i typed this: 'source /usr/local/gromacs/bin/GMXRC' after 'sudo make install' command . and then gmx grompp -h .and i can see GMXRC in this adress in my laptop.is everything right? but why dose not know gmx and it get this massage that program grompp is currently not

Re: [gmx-users] gromacs installation

Hi, On Mon, Jul 4, 2016 at 6:36 PM roshanak starlight wrote: > Should I remove gromacs that I've installed? > Depends which one you want to use. If you don't know, you want 5.1.2. > i don't understand what this means : source >

Re: [gmx-users] gromacs installation

Should I remove gromacs that I've installed? i don't understand what this means : source /your/installation/prefix/here/bin/GMXRC On Mon, Jul 4, 2016 at 5:03 PM, Mark Abraham wrote: > Hi, > > You need to teach your shell which version of GROMACS you want to use, or >

Re: [gmx-users] gromacs installation

Hi, You need to teach your shell which version of GROMACS you want to use, or it will do what it can from the existing environment. For example, http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#getting-access-to-gromacs-after-installation Mark On Mon, Jul 4, 2016 at 2:05

[gmx-users] gromacs installation

hello i try to install gromacs in my laptop with this cpu :AMD Dual-core processor E-350 and Linux operating system ubuntu 14.04 i installed gromacs-5.1.2 and gromacs-5 but both of these versions get error about grompp .and installation from software center (gromacs-4.5.6) get this error:

Re: [gmx-users] Gromacs installation.

http://gerrit.gromacs.org/download/regressiontests-5.0.4.tar.gz I think that something makes this link not downloadable. When I disable the download from -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON by deleting -DREGRESSIONTEST_DOWNLOAD=ON asking me to make GMX_BUILD_UNITTESTS=ON Then

Re: [gmx-users] Gromacs installation.

With that amount of information it'll be hard for anyone to diagnose your issue -- unless someone else ran into the same problem. If you want help you need to i) try hard ii) try harder iii) describe what you tried and you failed. -- Szilárd On Fri, May 13, 2016 at 12:53 PM, Elsaid Younes

[gmx-users] Gromacs installation.

Hi all, I have installed gromacs like the quick and dirty installation. I have a 16.04 version of ubuntu. I can not start it. I used to do the same procedure in ubuntu 15.10, and it worked fine. /Elsaid -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Gromacs Installation

Thanks. - Original Message - From: "Justin Lemkul" <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Tuesday, April 12, 2016 4:54:19 PM Subject: Re: [gmx-users] Gromacs Installation On 4/12/16 7:08 AM, ABANTIKA PAL wrote: > Hi, > > I have installed GROMACS 5.1.

Re: [gmx-users] Gromacs Installation

On 4/12/16 7:08 AM, ABANTIKA PAL wrote: Hi, I have installed GROMACS 5.1.2 by performing the steps described in the installation guide. All the steps have been executed successfully. But, no executable of mdrun is created in the build folder. Moreover, upon executing "which gromacs", its

[gmx-users] Gromacs Installation

Hi, I have installed GROMACS 5.1.2 by performing the steps described in the installation guide. All the steps have been executed successfully. But, no executable of mdrun is created in the build folder. Moreover, upon executing "which gromacs", its showing no gromacs in

Re: [gmx-users] Gromacs installation FTP issue

Hi, Yes, you could have simply changed the ftp:// prefix to http:// and it would have been fine. Future releases will likely offer both styles of link. The regressiontest download is only available with http for now, so your problem there was not related to FTP limitations. Mark On Wed, Feb 10,

[gmx-users] Gromacs installation FTP issue

Hi Everyone, I am trying to install the latest version of Gromacs. Before, I mention the real question I have to let you know that our system admin has diabled FTP downloads. (Don't ask me why, but all FTP usages in the campus are banned) So, thanks to a Chrome extension I was able to download

Re: [gmx-users] Gromacs installation FTP issue

Hi, I was able to troubleshoot it and install Gromacs successfully, by pointing the installation dir of regression tests. cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_PATH=/home/ bi/Desktop/gromacs-5.1.2/build/regressiontests-5.1.2 Thanks On Wed, Feb 10, 2016 at 10:28 AM, Ragothaman

Re: [gmx-users] gromacs installation fatal errors

On 4/22/15 10:26 PM, Brett wrote: Dear All, I just tried to install gromacs-5.0.4, and I got 2 fatal errors: 1. /gromacs-5.0.4/build/CMakeFiles/CmakeTmp/CheckIncludeFiles:c:16 fata error:io.h: No such file or directory 2. . /gromacs-5.0.4/Src/gromacs/legacyheader No such file or

Re: [gmx-users] Gromacs Installation problem

Thanks Mark. Your guess is right. It works. Regards, Shankar On Fri, Jan 9, 2015 at 7:41 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Last time I saw something like that, the person was trying to build in and install to the same place. Sharing your cmake command line would have been

Re: [gmx-users] Gromacs Installation problem

Hi, Last time I saw something like that, the person was trying to build in and install to the same place. Sharing your cmake command line would have been a good idea. Mark On Jan 9, 2015 2:27 PM, Shankar Prasad Kanaujia spkanau...@gmail.com wrote: Dear Users, I am getting a unique problem

[gmx-users] Gromacs Installation problem

Dear Users, I am getting a unique problem while installing gromacs. I am able to install any version of gromacs in the default path (i.e. /usr/local/gromacs). However, if I specify any other location by -DCMAKE_INSTALL_PREFIX=/home/user/softwares/GMX_5.0.4, I get the following error: !-- CMake

[gmx-users] gromacs installation

Dear Gromacs users I install gromacs version 5.0.2 by this command line:cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON but I received an error that showed regression tests and it's link is inactive. please help me , how can I install gromacs without regression test by cmake?