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

[Netaly Khazanov]

Thank you for trying to help me. I will take into account all your comments.

On Sun, Apr 26, 2020 at 6:18 PM lazaro monteserin <
lamonteserincastan...@gmail.com> wrote:

> Hey Netaly, are you trying to install Gromacs 2019 and 2020 at the same
> time? If not a couple of things to keep in mind.  Be sure before installing
> Gromacs you have all the utilities that Gromacs use, compilers, etc and
> that their versions are supported. I saw you are trying to install it for
> GPU, for that you need to install first the cuda toolkit versión for your
> linux. Now if you are installing Gromacs in an Ubuntu virtual machine on
> windows this is going to be a big problem. So for this case my
> recommendation is install it without GPU. Follow the instructions for
> installation in the website. Should work perfectly. Kindly, Lazaro
>
> On Sun, Apr 26, 2020 at 12:07 PM Yu Du  wrote:
>
> > Hi Netaly,
> >
> > Although I do not know the exact reason of the failure, after skimming
> > through your command, I think that you probably need to assign absolute
> > path to CMAKE_INSTALL_PREFIX and have access to the internet for
> > downloading REGRESSIONTEST and FFTW package.
> >
> > If you are new to GROMACS, I recommend installation from simple case,
> such
> > as only CPU no GPU. Only after successfully installing CPU only version
> > GROMACS, run to the next level CPU+GPU. This step-by-step installation
> > practice can give you a feeling of choosing CMake options.
> >
> > Cheers,
> >
> > Du, Yu
> > PhD Student,
> > Shanghai Institute of Organic Chemistry
> > 345 Ling Ling Rd., Shanghai, China.
> > Zip: 200032, Tel: (86) 021 5492 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 for GROMACS users 
> > Subject: [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
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3
> > -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc
> > -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
> > -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
> > I've used gcc 5 version (tried also 6 version)
> >
> > However, I am struggling through make execution :
> > in gromacs 2019 -
> >
> > [ 37%] Built target libgromacs_generated
> > [ 37%] Built target libgromacs_external
> > Scanning dependencies of target gpu_utilstest_cuda
> > [ 37%] Linking CXX shared library
> ../../../../lib/libgpu_utilstest_cuda.so
> > [ 37%] Built target gpu_utilstest_cuda
> >
> > in gromacs 2020-
> > [ 27%] Built target linearalgebra
> > [ 27%] Built target scanner
> > [ 27%] Built target tng_io_obj
> > [ 27%] Built target modularsimulator
> >
> > It just stuck on the line and doesn't continue to run.
> >
> > Any suggestions will be appreciated.
> > Thanks in advance.
> >
> >
> > --
> > Netaly
> > --
> > 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!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at
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> posting!
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-- 
Netaly
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Re: [gmx-users] gromacs installation (2020&2019)

[lazaro monteserin]

Hey Netaly, are you trying to install Gromacs 2019 and 2020 at the same
time? If not a couple of things to keep in mind.  Be sure before installing
Gromacs you have all the utilities that Gromacs use, compilers, etc and
that their versions are supported. I saw you are trying to install it for
GPU, for that you need to install first the cuda toolkit versión for your
linux. Now if you are installing Gromacs in an Ubuntu virtual machine on
windows this is going to be a big problem. So for this case my
recommendation is install it without GPU. Follow the instructions for
installation in the website. Should work perfectly. Kindly, Lazaro

On Sun, Apr 26, 2020 at 12:07 PM Yu Du  wrote:

> Hi Netaly,
>
> Although I do not know the exact reason of the failure, after skimming
> through your command, I think that you probably need to assign absolute
> path to CMAKE_INSTALL_PREFIX and have access to the internet for
> downloading REGRESSIONTEST and FFTW package.
>
> If you are new to GROMACS, I recommend installation from simple case, such
> as only CPU no GPU. Only after successfully installing CPU only version
> GROMACS, run to the next level CPU+GPU. This step-by-step installation
> practice can give you a feeling of choosing CMake options.
>
> Cheers,
>
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 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 for GROMACS users 
> Subject: [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
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc
> -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
> -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
> I've used gcc 5 version (tried also 6 version)
>
> However, I am struggling through make execution :
> in gromacs 2019 -
>
> [ 37%] Built target libgromacs_generated
> [ 37%] Built target libgromacs_external
> Scanning dependencies of target gpu_utilstest_cuda
> [ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so
> [ 37%] Built target gpu_utilstest_cuda
>
> in gromacs 2020-
> [ 27%] Built target linearalgebra
> [ 27%] Built target scanner
> [ 27%] Built target tng_io_obj
> [ 27%] Built target modularsimulator
>
> It just stuck on the line and doesn't continue to run.
>
> Any suggestions will be appreciated.
> Thanks in advance.
>
>
> --
> Netaly
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
> --
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] gromacs installation (2020&2019)

[Yu Du]

Hi Netaly,

Although I do not know the exact reason of the failure, after skimming through 
your command, I think that you probably need to assign absolute path to 
CMAKE_INSTALL_PREFIX and have access to the internet for downloading 
REGRESSIONTEST and FFTW package.

If you are new to GROMACS, I recommend installation from simple case, such as 
only CPU no GPU. Only after successfully installing CPU only version GROMACS, 
run to the next level CPU+GPU. This step-by-step installation practice can give 
you a feeling of choosing CMake options.

Cheers,

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275

From: 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 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
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3
-DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc
-DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
-DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
I've used gcc 5 version (tried also 6 version)

However, I am struggling through make execution :
in gromacs 2019 -

[ 37%] Built target libgromacs_generated
[ 37%] Built target libgromacs_external
Scanning dependencies of target gpu_utilstest_cuda
[ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so
[ 37%] Built target gpu_utilstest_cuda

in gromacs 2020-
[ 27%] Built target linearalgebra
[ 27%] Built target scanner
[ 27%] Built target tng_io_obj
[ 27%] Built target modularsimulator

It just stuck on the line and doesn't continue to run.

Any suggestions will be appreciated.
Thanks in advance.


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

[Netaly Khazanov]

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
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3
-DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc
-DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
-DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
I've used gcc 5 version (tried also 6 version)

However, I am struggling through make execution :
in gromacs 2019 -

[ 37%] Built target libgromacs_generated
[ 37%] Built target libgromacs_external
Scanning dependencies of target gpu_utilstest_cuda
[ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so
[ 37%] Built target gpu_utilstest_cuda

in gromacs 2020-
[ 27%] Built target linearalgebra
[ 27%] Built target scanner
[ 27%] Built target tng_io_obj
[ 27%] Built target modularsimulator

It just stuck on the line and doesn't continue to run.

Any suggestions will be appreciated.
Thanks in advance.


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

[Groenhof, Gerrit]

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

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 would be appreciated.

Thank you.
Best
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[gmx-users] Gromacs installation to do coupled QMMM with Gaussian

[Maryam Kowsar]

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 would be appreciated.

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

[Benson Muite]

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? 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 gromacs-2016.4.tar.gz
cd gromacs-2016.4/
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=on -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on 
-DCMAKE_INSTALL_PREFIX=~/
gromacs-2016.4/
make

*error message
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘int ddcoord2ddnodeid(gmx_domdec_t*, int*)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:233:53: 
error: ‘MPI_Cart_rank’ was not declared in this scope
  MPI_Cart_rank(dd->mpi_comm_all, c, );
  ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘void dd_collect_vec_sendrecv(gmx_domdec_t*, real (*)[3], real 
(*)[3])’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1185:47: 
error: ‘MPI_STATUS_IGNORE’ was not declared in this scope
   n, dd->mpi_comm_all, MPI_STATUS_IGNORE);
^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘void dd_distribute_vec_sendrecv(gmx_domdec_t*, t_block*, real (*)[3], 
real (*)[3])’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1472:49: 
error: ‘MPI_STATUS_IGNORE’ was not declared in this scope
   MPI_ANY_TAG, dd->mpi_comm_all, MPI_STATUS_IGNORE);
  ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘int ddcoord2simnodeid(t_commrec*, int, int, int)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1937:58: 
error: ‘MPI_Cart_rank’ was not declared in this scope
  MPI_Cart_rank(cr->mpi_comm_mysim, coords, );
   ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘int dd_simnode2pmenode(const gmx_domdec_t*, const t_commrec*, int)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1976:67: 
error: ‘MPI_Cart_coords’ was not declared in this scope
  MPI_Cart_coords(cr->mpi_comm_mysim, sim_nodeid, DIM, coord);
^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1981:66: 
error: ‘MPI_Cart_rank’ was not declared in this scope
  MPI_Cart_rank(cr->mpi_comm_mysim, coord_pme, );
   ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘gmx_bool receive_vir_ener(const gmx_domdec_t*, const t_commrec*)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:2106:76: 
error: ‘MPI_Cart_coords’ was not declared in this scope
  MPI_Cart_coords(cr->mpi_comm_mysim, cr->sim_nodeid, DIM, coords);
 ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:2111:64: 
error: ‘MPI_Cart_rank’ was not declared in this scope
  MPI_Cart_rank(cr->mpi_comm_mysim, coords, );
 ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘void make_pp_communicator(FILE*, gmx_domdec_t*, t_commrec*, int)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5642:35: 
error: ‘MPI_Cart_create’ was not declared in this scope
  _cart);
^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5682:64: 
error: ‘MPI_Cart_coords’ was not declared in this scope
  MPI_Cart_coords(dd->mpi_comm_all, dd->rank, DIM, dd->ci);
 ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5706:79: 
error: ‘MPI_Cart_rank’ was not declared in this scope
  MPI_Cart_rank(dd->mpi_comm_all, dd->master_ci, 
>masterrank);

^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘void split_communicator(FILE*, t_commrec*, gmx_domdec_t*, int, int)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5862:35: 
error: ‘MPI_Cart_create’ was not declared in this scope
  _cart);
^

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

[郭聪]

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 gromacs-2016.4.tar.gz
cd gromacs-2016.4/
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=on -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on 
-DCMAKE_INSTALL_PREFIX=~/
gromacs-2016.4/
make

*error message
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘int ddcoord2ddnodeid(gmx_domdec_t*, int*)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:233:53: 
error: ‘MPI_Cart_rank’ was not declared in this scope
 MPI_Cart_rank(dd->mpi_comm_all, c, );
 ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘void dd_collect_vec_sendrecv(gmx_domdec_t*, real (*)[3], real 
(*)[3])’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1185:47: 
error: ‘MPI_STATUS_IGNORE’ was not declared in this scope
  n, dd->mpi_comm_all, MPI_STATUS_IGNORE);
   ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘void dd_distribute_vec_sendrecv(gmx_domdec_t*, t_block*, real (*)[3], 
real (*)[3])’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1472:49: 
error: ‘MPI_STATUS_IGNORE’ was not declared in this scope
  MPI_ANY_TAG, dd->mpi_comm_all, MPI_STATUS_IGNORE);
 ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘int ddcoord2simnodeid(t_commrec*, int, int, int)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1937:58: 
error: ‘MPI_Cart_rank’ was not declared in this scope
 MPI_Cart_rank(cr->mpi_comm_mysim, coords, );
  ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘int dd_simnode2pmenode(const gmx_domdec_t*, const t_commrec*, int)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1976:67: 
error: ‘MPI_Cart_coords’ was not declared in this scope
 MPI_Cart_coords(cr->mpi_comm_mysim, sim_nodeid, DIM, coord);
   ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1981:66: 
error: ‘MPI_Cart_rank’ was not declared in this scope
 MPI_Cart_rank(cr->mpi_comm_mysim, coord_pme, );
  ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘gmx_bool receive_vir_ener(const gmx_domdec_t*, const t_commrec*)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:2106:76: 
error: ‘MPI_Cart_coords’ was not declared in this scope
 MPI_Cart_coords(cr->mpi_comm_mysim, cr->sim_nodeid, DIM, coords);
^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:2111:64: 
error: ‘MPI_Cart_rank’ was not declared in this scope
 MPI_Cart_rank(cr->mpi_comm_mysim, coords, );
^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘void make_pp_communicator(FILE*, gmx_domdec_t*, t_commrec*, int)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5642:35: 
error: ‘MPI_Cart_create’ was not declared in this scope
 _cart);
   ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5682:64: 
error: ‘MPI_Cart_coords’ was not declared in this scope
 MPI_Cart_coords(dd->mpi_comm_all, dd->rank, DIM, dd->ci);
^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5706:79: 
error: ‘MPI_Cart_rank’ was not declared in this scope
 MPI_Cart_rank(dd->mpi_comm_all, dd->master_ci, 
>masterrank);
   ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In 
function ‘void split_communicator(FILE*, t_commrec*, gmx_domdec_t*, int, int)’:
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5862:35: 
error: ‘MPI_Cart_create’ was not declared in this scope
 _cart);
   ^
/gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5875:72: 
error: ‘MPI_Cart_coords’ was not declared in this scope
 MPI_Cart_coords(cr->mpi_comm_mysim, cr->sim_nodeid, DIM, 

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

[Jia Hong]

My bad, I missed a line in the warning message:

Building NVCC (Device) object 
src/gromac/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj

   CMake Warning (dev) at 
libgromacs_generated_nbnxn_cuda.cu.obj.Release.cmake:74:
   Syntax Warning in cmake code at column 28


   Argument not separated from preceding token by whitespace.
 This warning is for project developers. Use -Wno-dev to suppress it.






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Jia Hong 

Sent: Wednesday, May 30, 2018 9:28 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. Here is the error 
message in Visual studio 2015

CMake Error at libgromacs_generated_nbnxn_cuda.cu.obj.Release.cmake:223 
(message):
 Error generating
 
C:/tools/GROMACS/gromacs-2018.1/build_gpu/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj


If this is of any use, there's also an accompanying warning message appearing 
right before the error message I showed above:

Building NVCC (Device) object 
src/gromac/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj
   Syntax Warning in cmake code at column 28
   Argument not separated from preceding token by whitespace.
 This warning is for project developers. Use -Wno-dev to suppress it.

The system specs I'm using:

  *   Windows 7
  *   VS 2015
 *   VS 2015 developer prompt to manually compile the file CMake was trying 
to compile
  *   CMake 3.11 GUI
  *   CUDA v9.1 - I've verified my CUDA installation with the provided build 
examples.
  *   Graphics card: GTX 1080


I do not know if CMake deals with whitespace paths, but when compiling 
manually, I had to make sure to add quotes around my cuda path and my --ccbin 
path because they are installed in directories with whitespaces.

Any help would be greatly appreciated.

Regards,
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 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
Bug #2509: Gromacs 2018 does not compile on Windows with CUDA - GROMACS - 
GROMACS development<https://redmine.gromacs.org/issues/2509>
redmine.gromacs.org
Redmine



Bug #2509: Gromacs 2018 does not compile on Windows with CUDA - GROMACS - 
GROMACS development<https://redmine.gromacs.org/issues/2509>
redmine.gromacs.org
Redmine



will be fixed in Gromacs 2018.2.
Meanwhile you can easily fix it yourself.
The line 646 of your src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu looks like
stat = cudaStreamQuery(stream);
and you only have to remove the unused (and undeclared) "stat = " variable,
turning the line into:
cudaStreamQuery(stream);
Please don't hesitate to report if there are any more errors :-)

Cheers,
Aleksei

On Tue, May 22, 2018 at 3:26 AM, Jia Hong  wrote:

> 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 CMake complains
> that "Check for working NVCC/C compiler combination - broken" and "CUDA
> compiler does not seem to be functional".
>  *   The solution was to surround the path with quotes in
> CUDA_TOOLKIT_ROOT_DIR
>   2.  Visual Studio fails to compile libgromacs (VS complains that it
> could not find ../../lib/gromacs.lib
>
>
> With regards to (2.), CMake completed the generation of VS build files
> without errors and I tried building it using VS 14 2015 (as specified in my
> CMake generation tool). The steps I took:
>
>   1.  set the build type to Release
>   2.  click build all
>
>
> I also tried compiling Gromacs with the exact same steps, but without GPU
> support, and it went without a hitch.
>
>
> I therefore suspect that it might be that "path issue" I faced earlier
> (1.), so I tried identifying the first error in VS build and it lead me to
> src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu.
>
>
> I copied the commands as-is within the makefile and tried t

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

[Jia Hong]

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. Here is the error 
message in Visual studio 2015

CMake Error at libgromacs_generated_nbnxn_cuda.cu.obj.Release.cmake:223 
(message):
 Error generating
 
C:/tools/GROMACS/gromacs-2018.1/build_gpu/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj


If this is of any use, there's also an accompanying warning message appearing 
right before the error message I showed above:

Building NVCC (Device) object 
src/gromac/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj
   Syntax Warning in cmake code at column 28
   Argument not separated from preceding token by whitespace.
 This warning is for project developers. Use -Wno-dev to suppress it.

The system specs I'm using:

  *   Windows 7
  *   VS 2015
 *   VS 2015 developer prompt to manually compile the file CMake was trying 
to compile
  *   CMake 3.11 GUI
  *   CUDA v9.1 - I've verified my CUDA installation with the provided build 
examples.
  *   Graphics card: GTX 1080


I do not know if CMake deals with whitespace paths, but when compiling 
manually, I had to make sure to add quotes around my cuda path and my --ccbin 
path because they are installed in directories with whitespaces.

Any help would be greatly appreciated.

Regards,
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 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
Bug #2509: Gromacs 2018 does not compile on Windows with CUDA - GROMACS - 
GROMACS development<https://redmine.gromacs.org/issues/2509>
redmine.gromacs.org
Redmine



will be fixed in Gromacs 2018.2.
Meanwhile you can easily fix it yourself.
The line 646 of your src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu looks like
stat = cudaStreamQuery(stream);
and you only have to remove the unused (and undeclared) "stat = " variable,
turning the line into:
cudaStreamQuery(stream);
Please don't hesitate to report if there are any more errors :-)

Cheers,
Aleksei

On Tue, May 22, 2018 at 3:26 AM, Jia Hong  wrote:

> 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 CMake complains
> that "Check for working NVCC/C compiler combination - broken" and "CUDA
> compiler does not seem to be functional".
>  *   The solution was to surround the path with quotes in
> CUDA_TOOLKIT_ROOT_DIR
>   2.  Visual Studio fails to compile libgromacs (VS complains that it
> could not find ../../lib/gromacs.lib
>
>
> With regards to (2.), CMake completed the generation of VS build files
> without errors and I tried building it using VS 14 2015 (as specified in my
> CMake generation tool). The steps I took:
>
>   1.  set the build type to Release
>   2.  click build all
>
>
> I also tried compiling Gromacs with the exact same steps, but without GPU
> support, and it went without a hitch.
>
>
> I therefore suspect that it might be that "path issue" I faced earlier
> (1.), so I tried identifying the first error in VS build and it lead me to
> src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu.
>
>
> I copied the commands as-is within the makefile and tried to compile it in
> VS developer command prompt myself.
>
>
> The error I got was:
>
> C:/tools/GROMACS/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/nvnxn_cuda.cu(646):
> error: expression must be a modifiable lvalue.
>
>
>
> My suspicion is that:
>
>   1.  The error "might" be because of a path problem ? (like before)
>   2.  nvnxn_cuda.cu at line 646 has a syntax error. (maybe)
>
>
> Any help would be greatly appreciated.
>
>
> Regards,
>
> Harry.
>
> --
> 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_g

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

[Aleksei Iupinov]

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 2018.2.
Meanwhile you can easily fix it yourself.
The line 646 of your src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu looks like
stat = cudaStreamQuery(stream);
and you only have to remove the unused (and undeclared) "stat = " variable,
turning the line into:
cudaStreamQuery(stream);
Please don't hesitate to report if there are any more errors :-)

Cheers,
Aleksei

On Tue, May 22, 2018 at 3:26 AM, Jia Hong  wrote:

> 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 CMake complains
> that "Check for working NVCC/C compiler combination - broken" and "CUDA
> compiler does not seem to be functional".
>  *   The solution was to surround the path with quotes in
> CUDA_TOOLKIT_ROOT_DIR
>   2.  Visual Studio fails to compile libgromacs (VS complains that it
> could not find ../../lib/gromacs.lib
>
>
> With regards to (2.), CMake completed the generation of VS build files
> without errors and I tried building it using VS 14 2015 (as specified in my
> CMake generation tool). The steps I took:
>
>   1.  set the build type to Release
>   2.  click build all
>
>
> I also tried compiling Gromacs with the exact same steps, but without GPU
> support, and it went without a hitch.
>
>
> I therefore suspect that it might be that "path issue" I faced earlier
> (1.), so I tried identifying the first error in VS build and it lead me to
> src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu.
>
>
> I copied the commands as-is within the makefile and tried to compile it in
> VS developer command prompt myself.
>
>
> The error I got was:
>
> C:/tools/GROMACS/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/nvnxn_cuda.cu(646):
> error: expression must be a modifiable lvalue.
>
>
>
> My suspicion is that:
>
>   1.  The error "might" be because of a path problem ? (like before)
>   2.  nvnxn_cuda.cu at line 646 has a syntax error. (maybe)
>
>
> Any help would be greatly appreciated.
>
>
> Regards,
>
> Harry.
>
> --
> 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.
>
-- 
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* 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

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mail to gmx-users-requ...@gromacs.org.

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

[Jia Hong]

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 CMake complains that 
"Check for working NVCC/C compiler combination - broken" and "CUDA compiler 
does not seem to be functional".
 *   The solution was to surround the path with quotes in 
CUDA_TOOLKIT_ROOT_DIR
  2.  Visual Studio fails to compile libgromacs (VS complains that it could not 
find ../../lib/gromacs.lib


With regards to (2.), CMake completed the generation of VS build files without 
errors and I tried building it using VS 14 2015 (as specified in my CMake 
generation tool). The steps I took:

  1.  set the build type to Release
  2.  click build all


I also tried compiling Gromacs with the exact same steps, but without GPU 
support, and it went without a hitch.


I therefore suspect that it might be that "path issue" I faced earlier (1.), so 
I tried identifying the first error in VS build and it lead me to 
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu.


I copied the commands as-is within the makefile and tried to compile it in VS 
developer command prompt myself.


The error I got was:

C:/tools/GROMACS/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/nvnxn_cuda.cu(646):
 error: expression must be a modifiable lvalue.



My suspicion is that:

  1.  The error "might" be because of a path problem ? (like before)
  2.  nvnxn_cuda.cu at line 646 has a syntax error. (maybe)


Any help would be greatly appreciated.


Regards,

Harry.

-- 
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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gromacs installation

[Wes Barnett]

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 utilized. How can I fully utilize
> the all 80 CPUs for mdrun.
>
> I have used below cmake command for the installation
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
> -DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> -DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs
>
> I have not seen any errors during installation.
>

You should go ahead and just install 2016.3 instead of 5.1.

What is your exact command when you run mdrun?

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
-- 
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
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] gromacs installation

[vijayakumar gosu]

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 installation

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
-DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
-DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs

I have not seen any errors during installation.

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

[Szilárd Páll]

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 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
> eral;dl;general;rt;general;m;general;gmxfftw;general;-lpthr
> ead;general;-fopenmp;
>

Yeah, that's what I was expecting to see there, so not sure what was wrong.


>
>
> S. Mostafa Razavi
> Graduate Research Assistant
> Molecular Simulation Lab
> Department of Chemical and Biomolecular Engineering
> The University of Akron, OH, USA
>
> On Fri, Jul 7, 2017 at 2:36 PM, Szilárd Páll 
> wrote:
>
> > 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 that libgromacs.so is linked against the OpenMP
> > library, can you check what's in the libgromacs_LIB_DEPENDS variable in
> > CMakeCache.txt?
> >
> >
> > --
> > Szilárd
> >
> > On Fri, Jul 7, 2017 at 8:13 PM, Seyed Mostafa Razavi <
> s...@zips.uakron.edu
> > >
> > wrote:
> >
> > > 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 
> > > wrote:
> > >
> > > > 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 <
> > > > s...@zips.uakron.edu>
> > > > wrote:
> > > >
> > > > > 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
> > > > error.
> > > > >
> > > > > [Ahmad@chem30 build]$ make
> > > > >
> > > > > .
> > > > > .(lots of output)
> > > > > .
> > > > >
> > > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > > > libgromacs.dir/__/external/
> > > > > tng_io/src/lib/tng_io.c.o
> > > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > > > libgromacs.dir/__/external/
> > > > > tng_io/src/lib/md5.c.o
> > > > > [ 97%] Building CXX object src/gromacs/CMakeFiles/
> > > > > libgromacs.dir/__/external/lmfit/lmmin.cpp.o
> > > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > libgromacs.dir/utility/
> > > > > baseversion-gen.c.o
> > > > > [ 97%] Linking CXX shared library ../../lib/libgromacs.so
> > > > > [ 97%] Built target libgromacs
> > > > > Scanning dependencies of target template
> > > > > [ 97%] Building CXX object share/template/CMakeFiles/
> > > > > template.dir/template.cpp.o
> > > > > [ 97%] Linking CXX executable ../../bin/template
> > > > > ../../lib/libgromacs.so.2.3.0: undefined reference to
> `GOMP_parallel'
> > > > > collect2: error: 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
> > > > >
> > > > > "make check" command gives me the following output:
> > > > >
> > > > > [Ahmad@chem30 build]$ make check
> > > > > Scanning dependencies of target mdrun_objlib
> > > > > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/md.cpp.o
> > > > > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/resource-division.cpp.o
> > > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/runner.cpp.o
> > > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/repl_ex.cpp.o
> > > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/mdrun.cpp.o
> > > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/membed.cpp.o
> > > > > [  1%] Built target mdrun_objlib
> > > > > [  2%] Built target fftwBuild
> > > > > [ 87%] Built target libgromacs
> > > > > Scanning dependencies of target view_objlib
> > > > > [ 87%] Building CXX object src/programs/CMakeFiles/view_
> > > > > 

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

[Seyed Mostafa Razavi]

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
eral;dl;general;rt;general;m;general;gmxfftw;general;-lpthr
ead;general;-fopenmp;


S. Mostafa Razavi
Graduate Research Assistant
Molecular Simulation Lab
Department of Chemical and Biomolecular Engineering
The University of Akron, OH, USA

On Fri, Jul 7, 2017 at 2:36 PM, Szilárd Páll  wrote:

> 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 that libgromacs.so is linked against the OpenMP
> library, can you check what's in the libgromacs_LIB_DEPENDS variable in
> CMakeCache.txt?
>
>
> --
> Szilárd
>
> On Fri, Jul 7, 2017 at 8:13 PM, Seyed Mostafa Razavi  >
> wrote:
>
> > 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 
> > wrote:
> >
> > > 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 <
> > > s...@zips.uakron.edu>
> > > wrote:
> > >
> > > > 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
> > > error.
> > > >
> > > > [Ahmad@chem30 build]$ make
> > > >
> > > > .
> > > > .(lots of output)
> > > > .
> > > >
> > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > > libgromacs.dir/__/external/
> > > > tng_io/src/lib/tng_io.c.o
> > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > > libgromacs.dir/__/external/
> > > > tng_io/src/lib/md5.c.o
> > > > [ 97%] Building CXX object src/gromacs/CMakeFiles/
> > > > libgromacs.dir/__/external/lmfit/lmmin.cpp.o
> > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > libgromacs.dir/utility/
> > > > baseversion-gen.c.o
> > > > [ 97%] Linking CXX shared library ../../lib/libgromacs.so
> > > > [ 97%] Built target libgromacs
> > > > Scanning dependencies of target template
> > > > [ 97%] Building CXX object share/template/CMakeFiles/
> > > > template.dir/template.cpp.o
> > > > [ 97%] Linking CXX executable ../../bin/template
> > > > ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> > > > collect2: error: 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
> > > >
> > > > "make check" command gives me the following output:
> > > >
> > > > [Ahmad@chem30 build]$ make check
> > > > Scanning dependencies of target mdrun_objlib
> > > > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > objlib.dir/mdrun/md.cpp.o
> > > > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > objlib.dir/mdrun/resource-division.cpp.o
> > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > objlib.dir/mdrun/runner.cpp.o
> > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > objlib.dir/mdrun/repl_ex.cpp.o
> > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > objlib.dir/mdrun/mdrun.cpp.o
> > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > objlib.dir/mdrun/membed.cpp.o
> > > > [  1%] Built target mdrun_objlib
> > > > [  2%] Built target fftwBuild
> > > > [ 87%] Built target libgromacs
> > > > Scanning dependencies of target view_objlib
> > > > [ 87%] Building CXX object src/programs/CMakeFiles/view_
> > > > objlib.dir/view/view.cpp.o
> > > > [ 87%] Built target view_objlib
> > > > Scanning dependencies of target gmx
> > > > [ 88%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o
> > > > [ 88%] Building CXX object src/programs/CMakeFiles/gmx.
> > > > dir/legacymodules.cpp.o
> > > > [ 88%] Linking CXX executable ../../bin/gmx
> > > > ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> > > > collect2: error: ld returned 1 exit status
> > > > make[3]: *** [bin/gmx] Error 1
> > > > make[2]: *** 

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

[Szilárd Páll]

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 that libgromacs.so is linked against the OpenMP
library, can you check what's in the libgromacs_LIB_DEPENDS variable in
CMakeCache.txt?


--
Szilárd

On Fri, Jul 7, 2017 at 8:13 PM, Seyed Mostafa Razavi 
wrote:

> 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 
> wrote:
>
> > 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 <
> > s...@zips.uakron.edu>
> > wrote:
> >
> > > 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
> > error.
> > >
> > > [Ahmad@chem30 build]$ make
> > >
> > > .
> > > .(lots of output)
> > > .
> > >
> > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > libgromacs.dir/__/external/
> > > tng_io/src/lib/tng_io.c.o
> > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > libgromacs.dir/__/external/
> > > tng_io/src/lib/md5.c.o
> > > [ 97%] Building CXX object src/gromacs/CMakeFiles/
> > > libgromacs.dir/__/external/lmfit/lmmin.cpp.o
> > > [ 97%] Building C object src/gromacs/CMakeFiles/
> libgromacs.dir/utility/
> > > baseversion-gen.c.o
> > > [ 97%] Linking CXX shared library ../../lib/libgromacs.so
> > > [ 97%] Built target libgromacs
> > > Scanning dependencies of target template
> > > [ 97%] Building CXX object share/template/CMakeFiles/
> > > template.dir/template.cpp.o
> > > [ 97%] Linking CXX executable ../../bin/template
> > > ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> > > collect2: error: 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
> > >
> > > "make check" command gives me the following output:
> > >
> > > [Ahmad@chem30 build]$ make check
> > > Scanning dependencies of target mdrun_objlib
> > > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > objlib.dir/mdrun/md.cpp.o
> > > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > objlib.dir/mdrun/resource-division.cpp.o
> > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > objlib.dir/mdrun/runner.cpp.o
> > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > objlib.dir/mdrun/repl_ex.cpp.o
> > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > objlib.dir/mdrun/mdrun.cpp.o
> > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > objlib.dir/mdrun/membed.cpp.o
> > > [  1%] Built target mdrun_objlib
> > > [  2%] Built target fftwBuild
> > > [ 87%] Built target libgromacs
> > > Scanning dependencies of target view_objlib
> > > [ 87%] Building CXX object src/programs/CMakeFiles/view_
> > > objlib.dir/view/view.cpp.o
> > > [ 87%] Built target view_objlib
> > > Scanning dependencies of target gmx
> > > [ 88%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o
> > > [ 88%] Building CXX object src/programs/CMakeFiles/gmx.
> > > dir/legacymodules.cpp.o
> > > [ 88%] Linking CXX executable ../../bin/gmx
> > > ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> > > collect2: error: ld returned 1 exit status
> > > make[3]: *** [bin/gmx] Error 1
> > > make[2]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
> > > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > > make: *** [check] Error 2
> > >
> > >
> > > Here are some other information about my system:
> > >
> > > [Ahmad@chem30 Downloads]$ cat /etc/centos-release
> > > CentOS release 6.5 (Final)
> > >
> > > [Ahmad@chem30 Downloads]$ echo |cpp -fopenmp -dM |grep -i open
> > > #define _OPENMP 200805
> > >
> > >
> > > [Ahmad@chem30 Downloads]$ cmake --version
> > > cmake version 3.5.0
> > >
> > > [Ahmad@chem30 Downloads]$ gcc --version
> > > gcc (GCC) 5.3.1 20160406 (Red Hat 5.3.1-6)
> > > Copyright (C) 2010 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.
> > >
> > > 

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

[Seyed Mostafa Razavi]

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  wrote:

> 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 <
> s...@zips.uakron.edu>
> wrote:
>
> > 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
> error.
> >
> > [Ahmad@chem30 build]$ make
> >
> > .
> > .(lots of output)
> > .
> >
> > [ 97%] Building C object src/gromacs/CMakeFiles/
> > libgromacs.dir/__/external/
> > tng_io/src/lib/tng_io.c.o
> > [ 97%] Building C object src/gromacs/CMakeFiles/
> > libgromacs.dir/__/external/
> > tng_io/src/lib/md5.c.o
> > [ 97%] Building CXX object src/gromacs/CMakeFiles/
> > libgromacs.dir/__/external/lmfit/lmmin.cpp.o
> > [ 97%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/utility/
> > baseversion-gen.c.o
> > [ 97%] Linking CXX shared library ../../lib/libgromacs.so
> > [ 97%] Built target libgromacs
> > Scanning dependencies of target template
> > [ 97%] Building CXX object share/template/CMakeFiles/
> > template.dir/template.cpp.o
> > [ 97%] Linking CXX executable ../../bin/template
> > ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> > collect2: error: 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
> >
> > "make check" command gives me the following output:
> >
> > [Ahmad@chem30 build]$ make check
> > Scanning dependencies of target mdrun_objlib
> > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > objlib.dir/mdrun/md.cpp.o
> > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > objlib.dir/mdrun/resource-division.cpp.o
> > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > objlib.dir/mdrun/runner.cpp.o
> > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > objlib.dir/mdrun/repl_ex.cpp.o
> > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > objlib.dir/mdrun/mdrun.cpp.o
> > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > objlib.dir/mdrun/membed.cpp.o
> > [  1%] Built target mdrun_objlib
> > [  2%] Built target fftwBuild
> > [ 87%] Built target libgromacs
> > Scanning dependencies of target view_objlib
> > [ 87%] Building CXX object src/programs/CMakeFiles/view_
> > objlib.dir/view/view.cpp.o
> > [ 87%] Built target view_objlib
> > Scanning dependencies of target gmx
> > [ 88%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o
> > [ 88%] Building CXX object src/programs/CMakeFiles/gmx.
> > dir/legacymodules.cpp.o
> > [ 88%] Linking CXX executable ../../bin/gmx
> > ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> > collect2: error: ld returned 1 exit status
> > make[3]: *** [bin/gmx] Error 1
> > make[2]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > make: *** [check] Error 2
> >
> >
> > Here are some other information about my system:
> >
> > [Ahmad@chem30 Downloads]$ cat /etc/centos-release
> > CentOS release 6.5 (Final)
> >
> > [Ahmad@chem30 Downloads]$ echo |cpp -fopenmp -dM |grep -i open
> > #define _OPENMP 200805
> >
> >
> > [Ahmad@chem30 Downloads]$ cmake --version
> > cmake version 3.5.0
> >
> > [Ahmad@chem30 Downloads]$ gcc --version
> > gcc (GCC) 5.3.1 20160406 (Red Hat 5.3.1-6)
> > Copyright (C) 2010 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.
> >
> > 
> > 
> > Thank you,
> > S. Mostafa Razavi
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> 

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

[Szilárd Páll]

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 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 error.
>
> [Ahmad@chem30 build]$ make
>
> .
> .(lots of output)
> .
>
> [ 97%] Building C object src/gromacs/CMakeFiles/
> libgromacs.dir/__/external/
> tng_io/src/lib/tng_io.c.o
> [ 97%] Building C object src/gromacs/CMakeFiles/
> libgromacs.dir/__/external/
> tng_io/src/lib/md5.c.o
> [ 97%] Building CXX object src/gromacs/CMakeFiles/
> libgromacs.dir/__/external/lmfit/lmmin.cpp.o
> [ 97%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/utility/
> baseversion-gen.c.o
> [ 97%] Linking CXX shared library ../../lib/libgromacs.so
> [ 97%] Built target libgromacs
> Scanning dependencies of target template
> [ 97%] Building CXX object share/template/CMakeFiles/
> template.dir/template.cpp.o
> [ 97%] Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> collect2: error: 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
>
> "make check" command gives me the following output:
>
> [Ahmad@chem30 build]$ make check
> Scanning dependencies of target mdrun_objlib
> [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/md.cpp.o
> [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/resource-division.cpp.o
> [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/runner.cpp.o
> [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/repl_ex.cpp.o
> [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/mdrun.cpp.o
> [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/membed.cpp.o
> [  1%] Built target mdrun_objlib
> [  2%] Built target fftwBuild
> [ 87%] Built target libgromacs
> Scanning dependencies of target view_objlib
> [ 87%] Building CXX object src/programs/CMakeFiles/view_
> objlib.dir/view/view.cpp.o
> [ 87%] Built target view_objlib
> Scanning dependencies of target gmx
> [ 88%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o
> [ 88%] Building CXX object src/programs/CMakeFiles/gmx.
> dir/legacymodules.cpp.o
> [ 88%] Linking CXX executable ../../bin/gmx
> ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> collect2: error: ld returned 1 exit status
> make[3]: *** [bin/gmx] Error 1
> make[2]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> make: *** [check] Error 2
>
>
> Here are some other information about my system:
>
> [Ahmad@chem30 Downloads]$ cat /etc/centos-release
> CentOS release 6.5 (Final)
>
> [Ahmad@chem30 Downloads]$ echo |cpp -fopenmp -dM |grep -i open
> #define _OPENMP 200805
>
>
> [Ahmad@chem30 Downloads]$ cmake --version
> cmake version 3.5.0
>
> [Ahmad@chem30 Downloads]$ gcc --version
> gcc (GCC) 5.3.1 20160406 (Red Hat 5.3.1-6)
> Copyright (C) 2010 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.
>
> 
> 
> Thank you,
> S. Mostafa Razavi
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] Gromacs installation fails in CentOS 6.5

[Seyed Mostafa Razavi]

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 error.

[Ahmad@chem30 build]$ make

.
.(lots of output)
.

[ 97%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/
tng_io/src/lib/tng_io.c.o
[ 97%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/
tng_io/src/lib/md5.c.o
[ 97%] Building CXX object src/gromacs/CMakeFiles/
libgromacs.dir/__/external/lmfit/lmmin.cpp.o
[ 97%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/utility/
baseversion-gen.c.o
[ 97%] Linking CXX shared library ../../lib/libgromacs.so
[ 97%] Built target libgromacs
Scanning dependencies of target template
[ 97%] Building CXX object share/template/CMakeFiles/
template.dir/template.cpp.o
[ 97%] Linking CXX executable ../../bin/template
../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
collect2: error: 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

"make check" command gives me the following output:

[Ahmad@chem30 build]$ make check
Scanning dependencies of target mdrun_objlib
[  0%] Building CXX object src/programs/CMakeFiles/mdrun_
objlib.dir/mdrun/md.cpp.o
[  0%] Building CXX object src/programs/CMakeFiles/mdrun_
objlib.dir/mdrun/resource-division.cpp.o
[  1%] Building CXX object src/programs/CMakeFiles/mdrun_
objlib.dir/mdrun/runner.cpp.o
[  1%] Building CXX object src/programs/CMakeFiles/mdrun_
objlib.dir/mdrun/repl_ex.cpp.o
[  1%] Building CXX object src/programs/CMakeFiles/mdrun_
objlib.dir/mdrun/mdrun.cpp.o
[  1%] Building CXX object src/programs/CMakeFiles/mdrun_
objlib.dir/mdrun/membed.cpp.o
[  1%] Built target mdrun_objlib
[  2%] Built target fftwBuild
[ 87%] Built target libgromacs
Scanning dependencies of target view_objlib
[ 87%] Building CXX object src/programs/CMakeFiles/view_
objlib.dir/view/view.cpp.o
[ 87%] Built target view_objlib
Scanning dependencies of target gmx
[ 88%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o
[ 88%] Building CXX object src/programs/CMakeFiles/gmx.
dir/legacymodules.cpp.o
[ 88%] Linking CXX executable ../../bin/gmx
../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
collect2: error: ld returned 1 exit status
make[3]: *** [bin/gmx] Error 1
make[2]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
make: *** [check] Error 2


Here are some other information about my system:

[Ahmad@chem30 Downloads]$ cat /etc/centos-release
CentOS release 6.5 (Final)

[Ahmad@chem30 Downloads]$ echo |cpp -fopenmp -dM |grep -i open
#define _OPENMP 200805


[Ahmad@chem30 Downloads]$ cmake --version
cmake version 3.5.0

[Ahmad@chem30 Downloads]$ gcc --version
gcc (GCC) 5.3.1 20160406 (Red Hat 5.3.1-6)
Copyright (C) 2010 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.



Thank you,
S. Mostafa Razavi
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Re: [gmx-users] Gromacs installation on GPU

[Mark Abraham]

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
inconvenient than a second GROMACS install when you later decide you need
GPU support.

Mark

On Wed, Mar 15, 2017 at 1:55 PM Justin Lemkul  wrote:

>
>
> 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 .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DGMX_MPI=ON -DGMX_GPU=OFF
> > make
> > make check
> > make install
> > source /usr/local/gromacs/bin/GMXRC
> >
> > -
> >
> > Now I want to do MD simulation on GPU.
> >
> > Should I do installation again? Isn't there a more simple way?
> >
>
> The install process requires information about the GPU compatibility of the
> hardware, libraries etc, so yes, if you used -DGMX_GPU=OFF then you need to
> install again (ideally with a current version of GROMACS, or at minimum the
> latest patch release in the 5.1 series, rather than an old version of the
> code).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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
>
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Re: [gmx-users] Gromacs installation on GPU

[Justin Lemkul]

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 .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_MPI=ON -DGMX_GPU=OFF
make
make check
make install
source /usr/local/gromacs/bin/GMXRC

-

Now I want to do MD simulation on GPU.

Should I do installation again? Isn't there a more simple way?



The install process requires information about the GPU compatibility of the 
hardware, libraries etc, so yes, if you used -DGMX_GPU=OFF then you need to 
install again (ideally with a current version of GROMACS, or at minimum the 
latest patch release in the 5.1 series, rather than an old version of the code).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Gromacs installation on GPU

[Andrew Bostick]

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 -DGMX_GPU=OFF
make
make check
make install
source /usr/local/gromacs/bin/GMXRC

-

Now I want to do MD simulation on GPU.

Should I do installation again? Isn't there a more simple way?

Best,
Andrew
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Re: [gmx-users] Gromacs installation on GPU

[Szilárd Páll]

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
>
>> 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 the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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[gmx-users] Gromacs installation on GPU

[Atila Petrosian]

*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*
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Re: [gmx-users] Gromacs installation on GPU

[Szilárd Páll]

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 -DGMX_GPU=ON
>
> -- The C compiler identification is GNU 4.4.7
> -- The CXX compiler identification is GNU 4.4.7
> -- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Looking for NVIDIA GPUs present in the system
> -- Number of NVIDIA GPUs detected: 1
> CUDA_TOOLKIT_ROOT_DIR not found or specified
> -- Could NOT find CUDA (missing:  CUDA_TOOLKIT_ROOT_DIR
> CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at
> least version "4.0")

^^^
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.

--
Szilárd

> CMake Error at cmake/gmxManageGPU.cmake:153 (message):
>   mdrun supports native GPU acceleration on NVIDIA hardware with compute
>   capability >= 2.0 (Fermi or later).  This requires the NVIDIA CUDA
> toolkit,
>   which was not found.  Its location can be hinted by setting the
>   CUDA_TOOLKIT_ROOT_DIR CMake option (does not work as an environment
>   variable).  The typical location would be /usr/local/cuda[-version].  Note
>   that CPU or GPU acceleration can be selected at runtime.
>
>   1 NVIDIA GPU(s) found in the system:
>
>   GeForce GTX 480
>
>   Compute capability information not available, consult the NVIDIA website:
>
>   https://developer.nvidia.com/cuda-gpus
> Call Stack (most recent call first):
>   CMakeLists.txt:185 (include)
>
> -- Configuring incomplete, errors occurred!
> See also "/home/host/nasb/gromacs-5.1.1/build/CMakeFiles/CMakeOutput.log".
>
> I am beginner in the installation of gromacs as parallel and on GPU.
>
> Please guide me to solve this problem.
>
> Best,
> Atila
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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Re: [gmx-users] Gromacs installation on GPU

[Nikhil Maroli]

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 .
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[gmx-users] Gromacs installation on GPU

[Atila Petrosian]

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 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Number of NVIDIA GPUs detected: 1
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing:  CUDA_TOOLKIT_ROOT_DIR
CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at
least version "4.0")
CMake Error at cmake/gmxManageGPU.cmake:153 (message):
  mdrun supports native GPU acceleration on NVIDIA hardware with compute
  capability >= 2.0 (Fermi or later).  This requires the NVIDIA CUDA
toolkit,
  which was not found.  Its location can be hinted by setting the
  CUDA_TOOLKIT_ROOT_DIR CMake option (does not work as an environment
  variable).  The typical location would be /usr/local/cuda[-version].  Note
  that CPU or GPU acceleration can be selected at runtime.

  1 NVIDIA GPU(s) found in the system:

  GeForce GTX 480

  Compute capability information not available, consult the NVIDIA website:

  https://developer.nvidia.com/cuda-gpus
Call Stack (most recent call first):
  CMakeLists.txt:185 (include)

-- Configuring incomplete, errors occurred!
See also "/home/host/nasb/gromacs-5.1.1/build/CMakeFiles/CMakeOutput.log".

I am beginner in the installation of gromacs as parallel and on GPU.

Please guide me to solve this problem.

Best,
Atila
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Re: [gmx-users] gromacs installation

[roshanak starlight]

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' 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 installed ?
>
> On Mon, Jul 4, 2016 at 9:27 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> On Mon, Jul 4, 2016 at 6:36 PM roshanak starlight <
>> starlight@gmail.com>
>> 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
>> > /your/installation/prefix/here/bin/GMXRC
>> >
>>
>> GROMACS got installed somewhere. It installed a script named GMXRC that
>> can
>> teach your shell to use that version of GROMACS for as long as it runs. By
>> default, GROMACS installs to /usr/local/gromacs so you'd use
>>
>> source /usr/local/gromacs/bin/GMXRC
>>
>> to say to your shell to use that one. But if you installed somewhere else,
>> you need to adapt to refer to the right GMXRC.
>>
>> Mark
>>
>>
>> > 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
>> > > 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 PM roshanak starlight <
>> > starlight@gmail.com
>> > > >
>> > > wrote:
>> > >
>> > > > 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: illegal instruction core dumped .
>> > > > Who knows what's the problem?
>> > > >
>> > > > one told me that :I think you would run gmx under admin or force
>> UBUNTU
>> > > to
>> > > > set gromacs in your path
>> > > > what shuld i do?
>> > > > --
>> > > > 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!
>> > >
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>> > >
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Re: [gmx-users] gromacs installation

[roshanak starlight]

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 installed ?

On Mon, Jul 4, 2016 at 9:27 PM, Mark Abraham 
wrote:

> 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
> > /your/installation/prefix/here/bin/GMXRC
> >
>
> GROMACS got installed somewhere. It installed a script named GMXRC that can
> teach your shell to use that version of GROMACS for as long as it runs. By
> default, GROMACS installs to /usr/local/gromacs so you'd use
>
> source /usr/local/gromacs/bin/GMXRC
>
> to say to your shell to use that one. But if you installed somewhere else,
> you need to adapt to refer to the right GMXRC.
>
> Mark
>
>
> > 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
> > > 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 PM roshanak starlight <
> > starlight@gmail.com
> > > >
> > > wrote:
> > >
> > > > 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: illegal instruction core dumped .
> > > > Who knows what's the problem?
> > > >
> > > > one told me that :I think you would run gmx under admin or force
> UBUNTU
> > > to
> > > > set gromacs in your path
> > > > what shuld i do?
> > > > --
> > > > 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.
> > > >
> > > --
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> > >
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> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] gromacs installation

[Mark Abraham]

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
> /your/installation/prefix/here/bin/GMXRC
>

GROMACS got installed somewhere. It installed a script named GMXRC that can
teach your shell to use that version of GROMACS for as long as it runs. By
default, GROMACS installs to /usr/local/gromacs so you'd use

source /usr/local/gromacs/bin/GMXRC

to say to your shell to use that one. But if you installed somewhere else,
you need to adapt to refer to the right GMXRC.

Mark


> 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
> > 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 PM roshanak starlight <
> starlight@gmail.com
> > >
> > wrote:
> >
> > > 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: illegal instruction core dumped .
> > > Who knows what's the problem?
> > >
> > > one told me that :I think you would run gmx under admin or force UBUNTU
> > to
> > > set gromacs in your path
> > > what shuld i do?
> > > --
> > > 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
> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] gromacs installation

[roshanak starlight]

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
> 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 PM roshanak starlight  >
> wrote:
>
> > 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: illegal instruction core dumped .
> > Who knows what's the problem?
> >
> > one told me that :I think you would run gmx under admin or force UBUNTU
> to
> > set gromacs in your path
> > what shuld i do?
> > --
> > 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.
> >
> --
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>
> * Please search the archive at
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> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] gromacs installation

[Mark Abraham]

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 PM roshanak starlight 
wrote:

> 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: illegal instruction core dumped .
> Who knows what's the problem?
>
> one told me that :I think you would run gmx under admin or force UBUNTU to
> set gromacs in your path
> what shuld i do?
> --
> 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
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] gromacs installation

[roshanak starlight]

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: illegal instruction core dumped .
Who knows what's the problem?

one told me that :I think you would run gmx under admin or force UBUNTU to
set gromacs in your path
what shuld i do?
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Re: [gmx-users] Gromacs installation.

[Elsaid Younes]

 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 after I made it, I still get this
Total Test time (real) = 165.57 sec
[100%] Built target run-ctest
[100%] Unit tests disabled
NOTE: Unit tests have not been run. You need to set GMX_BUILD_UNITTESTS=ON
if you want to build and run them.
[100%] Built target unittests-notice
[100%] Built target check..After all Gromacs can not start.



On Fri, May 13, 2016 at 12:53 PM, Elsaid Younes  wrote:

> 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
>
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Re: [gmx-users] Gromacs installation.

[Szilárd Páll]

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  wrote:

> 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
> --
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> * Please search the archive at
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[gmx-users] Gromacs installation.

[Elsaid Younes]

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
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Re: [gmx-users] Gromacs Installation

[ABANTIKA PAL]

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 5.1.2 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 
> (/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
> Please help how to resolve the issue.
>

The binary is called gmx.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Gromacs Installation

[Justin Lemkul]

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 
showing
  no gromacs in 
(/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
Please help how to resolve the issue.



The binary is called gmx.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Gromacs Installation

[ABANTIKA PAL]

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 
(/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
Please help how to resolve the issue.

Thanks and regards

Abantika
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Re: [gmx-users] Gromacs installation FTP issue

[Mark Abraham]

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, 2016 at 5:59 AM Ragothaman Yennamalli 
wrote:

> 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 the gromacs
> installation package using the browser.
> However, while installing I realized that Gromcas tried to download the
> regression tests package via FTP and it was unable to the installation was
> unsuccessful. I have downloaded the regressiontests package from the
> browser and trying to install it again.
>
> So, my question is: Can I install Gromacs by bypassign FTP downloads?
>
> Thanks for any input!
>
> Raghu
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>
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> posting!
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[gmx-users] Gromacs installation FTP issue

[Ragothaman Yennamalli]

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 the gromacs
installation package using the browser.
However, while installing I realized that Gromcas tried to download the
regression tests package via FTP and it was unable to the installation was
unsuccessful. I have downloaded the regressiontests package from the
browser and trying to install it again.

So, my question is: Can I install Gromacs by bypassign FTP downloads?

Thanks for any input!

Raghu
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Re: [gmx-users] Gromacs installation FTP issue

[Ragothaman Yennamalli]

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 Yennamalli <
ragotha...@gmail.com> wrote:

> 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 the gromacs
> installation package using the browser.
> However, while installing I realized that Gromcas tried to download the
> regression tests package via FTP and it was unable to the installation was
> unsuccessful. I have downloaded the regressiontests package from the
> browser and trying to install it again.
>
> So, my question is: Can I install Gromacs by bypassign FTP downloads?
>
> Thanks for any input!
>
> Raghu
>
>
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Re: [gmx-users] gromacs installation fatal errors

[Justin Lemkul]

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 directory.

I am looking forward to getting your reply on how to sove the issue.



Provide all your commands and copy and paste errors rather than retyping them.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Gromacs Installation problem

[Shankar Prasad Kanaujia]

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
 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 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 Error at src/programs/cmake_install.cmake:42 (file):
  file INSTALL cannot find /home/user/softwares/GMX_5.0.4/bin/gmx_mpi.
  Call Stack (most recent call first): src/cmake_install.cmake:40 (include)
  cmake_install.cmake:48 (include)
  --
 
  at the last step (i.e. make install).
 
  I tried almost everything available through Google search. I have tried
  with several versions of cmake both as root as well as user.
 
  I would really appreciate if any one can provide some hint to solve this
  problem.
 
  Regards,
  Shankar
 
 
 
  --
  Shankar Prasad Kanaujia, Ph.D.
  Assistant Professor
  Department of Biotechnology
  Indian Institute of Technology Guwahati
  Guwahati - 781039 Assam, India
  Tele: 0361 258 2228
  Fax:  0361 258 2249
  Email: spkanau...@iitg.ernet.in
  Homepage: http://www.iitg.ernet.in/spkanaujia/
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  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
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  send a mail to gmx-users-requ...@gromacs.org.
 
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 posting!

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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.




-- 
Shankar Prasad Kanaujia, Ph.D.
Assistant Professor
Department of Biotechnology
Indian Institute of Technology Guwahati
Guwahati - 781039 Assam, India
Tele: 0361 258 2228
Fax:  0361 258 2249
Email: spkanau...@iitg.ernet.in
Homepage: http://www.iitg.ernet.in/spkanaujia/
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Re: [gmx-users] Gromacs Installation problem

[Mark Abraham]

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 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 Error at src/programs/cmake_install.cmake:42 (file):
 file INSTALL cannot find /home/user/softwares/GMX_5.0.4/bin/gmx_mpi.
 Call Stack (most recent call first): src/cmake_install.cmake:40 (include)
 cmake_install.cmake:48 (include)
 --

 at the last step (i.e. make install).

 I tried almost everything available through Google search. I have tried
 with several versions of cmake both as root as well as user.

 I would really appreciate if any one can provide some hint to solve this
 problem.

 Regards,
 Shankar



 --
 Shankar Prasad Kanaujia, Ph.D.
 Assistant Professor
 Department of Biotechnology
 Indian Institute of Technology Guwahati
 Guwahati - 781039 Assam, India
 Tele: 0361 258 2228
 Fax:  0361 258 2249
 Email: spkanau...@iitg.ernet.in
 Homepage: http://www.iitg.ernet.in/spkanaujia/
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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 * 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.

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[gmx-users] Gromacs Installation problem

[Shankar Prasad Kanaujia]

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 Error at src/programs/cmake_install.cmake:42 (file):
file INSTALL cannot find /home/user/softwares/GMX_5.0.4/bin/gmx_mpi.
Call Stack (most recent call first): src/cmake_install.cmake:40 (include)
cmake_install.cmake:48 (include)
--

at the last step (i.e. make install).

I tried almost everything available through Google search. I have tried
with several versions of cmake both as root as well as user.

I would really appreciate if any one can provide some hint to solve this
problem.

Regards,
Shankar



-- 
Shankar Prasad Kanaujia, Ph.D.
Assistant Professor
Department of Biotechnology
Indian Institute of Technology Guwahati
Guwahati - 781039 Assam, India
Tele: 0361 258 2228
Fax:  0361 258 2249
Email: spkanau...@iitg.ernet.in
Homepage: http://www.iitg.ernet.in/spkanaujia/
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[gmx-users] gromacs installation

[Amir Khan]

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?


thanks alot

 
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