Re: [gmx-users] compile with intel compiler

[Rolly Ng]

Hi,
I use the following combination with Intel PSXE. It works and your problem
is likely related to the name of the Intel CXX compiler.

source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64
source /opt/intel/impi/2018.4.274/bin64/mpivars.sh
source /opt/intel/mkl/bin/mklvars.sh intel64

FLAGS="-xCORE-AVX2"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS;
cmake .. -DCMAKE_C_COMPILER=mpiicc \
-DCMAKE_CXX_COMPILER=mpiicpc \
-DCMAKE_INSTALL_PREFIX=/home/user/Gromacs/gromacs-2020/install \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_MPI=ON \
-DGMX_SIMD=AVX2_256 \
-DMPIEXEC=srun \
-DMPIEXEC_NUMPROC_FLAG=-n \
-DMPIEXEC_PREFLAGS= \
-DMPIEXEC_POSTFLAGS=
make -j 16
make install

On Fri, Mar 27, 2020 at 12:35 AM Schulz, Roland 
wrote:

> This isn't really a GROMACS question. You might need to set
> LD_LIBRARY_PATH manual. If you don't know how you should ask e.g. your
> cluster admin. Or you could  use a static build (see GROMACS install guide).
>
> Roland
>
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >  On Behalf Of Harry
> > Mark Greenblatt
> > Sent: Thursday, March 26, 2020 12:11 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] compile with intel compiler
> >
> > BS"D
> >
> >
> > Yes, indeed, that was the error.  I did try to define the
> > GMX_GPLUSPLUS_PATH, and have that point to a local install of gcc 6.4;
> that
> > worked to compile and install gromacs.  But when it came to executing the
> > program it couldn't find the libstdc++ for gcc 6.4.  This is on a
> cluster, and
> > when I have compiled gromacs in the past with gcc 6.4, I can set up the
> > environment by loading the gcc 6.4 module, but this of course displaces
> the
> > intel compiler module.  If I add the gcc 6.4 library path in the GMXRC
> file,
> > would that interfere with the intel stuff?
> >
> >
> > Thanks
> >
> >
> > Harry
> >
> >
> >
> >
> >
> > Harry M. Greenblatt
> > Associate Staff Scientist
> > Dept of Structural Biology
> > harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs
> > 5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&
> > URL=mailto%3aharry.greenblatt%40weizmann.ac.il>
> > Weizmann Institute of SciencePhone:  972-8-934-3625
> > 234 Herzl St.Facsimile:   972-8-934-4159
> > Rehovot, 76100
> > Israel
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >  on behalf of Schulz,
> > Roland 
> > Sent: Wednesday, March 25, 2020 10:25:24 PM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] compile with intel compiler
> >
> > Hi,
> >
> >
> > Are you referring to this type of error:
> >
> > -- Performing Test USING_LIBSTDCXX
> > -- Performing Test USING_LIBSTDCXX - Success CMake Error at
> > cmake/FindLibStdCpp.cmake:119 (message):
> >   Found g++ at /usr/bin/g++.  Its version is 4.8.5.  GROMACS requires at
> >   least version 5.1.  Please specify a different g++ using
> >   GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH.
> >
> > This is because GROMACS needs both a C++ compiler and a C++ standard
> > library. The Intel compiler doesn't come with a standard library but
> utilizes
> > libstdc++ for that. GROMACS automatically looks for the right version of
> g++
> > to find the proper version of libstdc++
> >
> > If you are referring to a different error please be more specific and
> post the
> > exact error.
> >
> > Roland
> >
> > > -Original Message-
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> > >  On Behalf Of Harry
> > > Mark Greenblatt
> > > Sent: Wednesday, March 25, 2020 3:46 AM
> > > To: gmx-us...@gromacs.org
> > > Subject: [gmx-users] compile with intel compiler
> > >
> > > BS"D
> > >
> > > Dear All,
> > >
> > >  I would like to compile Gromacs 2020 with an intel compiler;  I set
> > > the
> > > following:
> > >
> > > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -
> > DGMX_MPI=on
> > > -DGMX_BUILD_OWN_FFTW=OFF - DGMX_FFT_LIBRARY=mkl
> > > -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -
> > > DMKL_INCLUDE_DIR=$MKLROOT/include
> > >
> > > Despite the fact that I have told it to use the Intel C++ compile is
> > > (which it finds), it still looks and finds the system g++, which, of
> > > course is quite old.  If I have given it the name of a 

Re: [gmx-users] compile with intel compiler

[Schulz, Roland]

This isn't really a GROMACS question. You might need to set LD_LIBRARY_PATH 
manual. If you don't know how you should ask e.g. your cluster admin. Or you 
could  use a static build (see GROMACS install guide).

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>  On Behalf Of Harry
> Mark Greenblatt
> Sent: Thursday, March 26, 2020 12:11 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] compile with intel compiler
> 
> BS"D
> 
> 
> Yes, indeed, that was the error.  I did try to define the
> GMX_GPLUSPLUS_PATH, and have that point to a local install of gcc 6.4; that
> worked to compile and install gromacs.  But when it came to executing the
> program it couldn't find the libstdc++ for gcc 6.4.  This is on a cluster, and
> when I have compiled gromacs in the past with gcc 6.4, I can set up the
> environment by loading the gcc 6.4 module, but this of course displaces the
> intel compiler module.  If I add the gcc 6.4 library path in the GMXRC file,
> would that interfere with the intel stuff?
> 
> 
> Thanks
> 
> 
> Harry
> 
> 
> 
> 
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology
> harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs
> 5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&
> URL=mailto%3aharry.greenblatt%40weizmann.ac.il>
> Weizmann Institute of SciencePhone:  972-8-934-3625
> 234 Herzl St.Facsimile:   972-8-934-4159
> Rehovot, 76100
> Israel
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>  on behalf of Schulz,
> Roland 
> Sent: Wednesday, March 25, 2020 10:25:24 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] compile with intel compiler
> 
> Hi,
> 
> 
> Are you referring to this type of error:
> 
> -- Performing Test USING_LIBSTDCXX
> -- Performing Test USING_LIBSTDCXX - Success CMake Error at
> cmake/FindLibStdCpp.cmake:119 (message):
>   Found g++ at /usr/bin/g++.  Its version is 4.8.5.  GROMACS requires at
>   least version 5.1.  Please specify a different g++ using
>   GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH.
> 
> This is because GROMACS needs both a C++ compiler and a C++ standard
> library. The Intel compiler doesn't come with a standard library but utilizes
> libstdc++ for that. GROMACS automatically looks for the right version of g++
> to find the proper version of libstdc++
> 
> If you are referring to a different error please be more specific and post the
> exact error.
> 
> Roland
> 
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >  On Behalf Of Harry
> > Mark Greenblatt
> > Sent: Wednesday, March 25, 2020 3:46 AM
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] compile with intel compiler
> >
> > BS"D
> >
> > Dear All,
> >
> >  I would like to compile Gromacs 2020 with an intel compiler;  I set
> > the
> > following:
> >
> > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -
> DGMX_MPI=on
> > -DGMX_BUILD_OWN_FFTW=OFF - DGMX_FFT_LIBRARY=mkl
> > -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -
> > DMKL_INCLUDE_DIR=$MKLROOT/include
> >
> > Despite the fact that I have told it to use the Intel C++ compile is
> > (which it finds), it still looks and finds the system g++, which, of
> > course is quite old.  If I have given it the name of a C++ compiler, why is 
> > it
> looking for g++?
> >
> >
> >
> > Thanks
> >
> > Harry
> >
> >
> >
> > 
> > Harry M. Greenblatt
> > Associate Staff Scientist
> > Dept of Structural Biology
> > harry.greenbl...@weizmann.ac.il<mailto:harry.greenbl...@weizmann.ac.il>
> > Weizmann Institute of SciencePhone:  972-8-934-6340
> > 234 Herzl St.Facsimile:   972-8-934-3361
> > Rehovot, 7610001
> > Israel
> >
> > --
> > 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 befor

Re: [gmx-users] compile with intel compiler

[Harry Mark Greenblatt]

BS"D


Yes, indeed, that was the error.  I did try to define the GMX_GPLUSPLUS_PATH, 
and have that point to a local install of gcc 6.4; that worked to compile and 
install gromacs.  But when it came to executing the program it couldn't find 
the libstdc++ for gcc 6.4.  This is on a cluster, and when I have compiled 
gromacs in the past with gcc 6.4, I can set up the environment by loading the 
gcc 6.4 module, but this of course displaces the intel compiler module.  If I 
add the gcc 6.4 library path in the GMXRC file, would that interfere with the 
intel stuff?


Thanks


Harry





Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-3625
234 Herzl St.Facsimile:   972-8-934-4159
Rehovot, 76100
Israel

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Schulz, Roland 

Sent: Wednesday, March 25, 2020 10:25:24 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] compile with intel compiler

Hi,


Are you referring to this type of error:

-- Performing Test USING_LIBSTDCXX
-- Performing Test USING_LIBSTDCXX - Success
CMake Error at cmake/FindLibStdCpp.cmake:119 (message):
  Found g++ at /usr/bin/g++.  Its version is 4.8.5.  GROMACS requires at
  least version 5.1.  Please specify a different g++ using
  GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH.

This is because GROMACS needs both a C++ compiler and a C++ standard library. 
The Intel compiler doesn't come with a standard library but utilizes libstdc++ 
for that. GROMACS automatically looks for the right version of g++ to find the 
proper version of libstdc++

If you are referring to a different error please be more specific and post the 
exact error.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>  On Behalf Of Harry
> Mark Greenblatt
> Sent: Wednesday, March 25, 2020 3:46 AM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] compile with intel compiler
>
> BS”D
>
> Dear All,
>
>  I would like to compile Gromacs 2020 with an intel compiler;  I set the
> following:
>
> -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -
> DGMX_MPI=on  -DGMX_BUILD_OWN_FFTW=OFF -
> DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -
> DMKL_INCLUDE_DIR=$MKLROOT/include
>
> Despite the fact that I have told it to use the Intel C++ compile is (which it
> finds), it still looks and finds the system g++, which, of course is quite 
> old.  If I
> have given it the name of a C++ compiler, why is it looking for g++?
>
>
>
> Thanks
>
> Harry
>
>
>
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology
> harry.greenbl...@weizmann.ac.il<mailto:harry.greenbl...@weizmann.ac.il>
> Weizmann Institute of SciencePhone:  972-8-934-6340
> 234 Herzl St.Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
>
> --
> 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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Re: [gmx-users] compile with intel compiler

[Schulz, Roland]

Hi,


Are you referring to this type of error:

-- Performing Test USING_LIBSTDCXX
-- Performing Test USING_LIBSTDCXX - Success
CMake Error at cmake/FindLibStdCpp.cmake:119 (message):
  Found g++ at /usr/bin/g++.  Its version is 4.8.5.  GROMACS requires at
  least version 5.1.  Please specify a different g++ using
  GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH.

This is because GROMACS needs both a C++ compiler and a C++ standard library. 
The Intel compiler doesn't come with a standard library but utilizes libstdc++ 
for that. GROMACS automatically looks for the right version of g++ to find the 
proper version of libstdc++

If you are referring to a different error please be more specific and post the 
exact error.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>  On Behalf Of Harry
> Mark Greenblatt
> Sent: Wednesday, March 25, 2020 3:46 AM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] compile with intel compiler
> 
> BS”D
> 
> Dear All,
> 
>  I would like to compile Gromacs 2020 with an intel compiler;  I set the
> following:
> 
> -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -
> DGMX_MPI=on  -DGMX_BUILD_OWN_FFTW=OFF -
> DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -
> DMKL_INCLUDE_DIR=$MKLROOT/include
> 
> Despite the fact that I have told it to use the Intel C++ compile is (which it
> finds), it still looks and finds the system g++, which, of course is quite 
> old.  If I
> have given it the name of a C++ compiler, why is it looking for g++?
> 
> 
> 
> Thanks
> 
> Harry
> 
> 
> 
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology
> harry.greenbl...@weizmann.ac.il<mailto:harry.greenbl...@weizmann.ac.il>
> Weizmann Institute of SciencePhone:  972-8-934-6340
> 234 Herzl St.Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
> 
> --
> 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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Re: [gmx-users] compile with intel compiler

[Lyudmyla Dorosh]

Dear Harry,

I'm not an expert, but before running gromacs install I "sourced" all Intel
libraries, and specified SIMD for my processor:

source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/impi/2019.5.281/intel64/bin/mpivars.sh
source /opt/intel/mkl/bin/mklvars.sh intel64

sudo cmake .. -DGMX_FFT_LIBRARY=mkl -DCMAKE_INSTALL_PREFIX=$installDir
-DGMX_MPI=on -DGMX_OPENMP=on -DGMX_CYCLE_SUBCOUNTERS=on -DGMX_GPU=off
-DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/opt/intel/bin/icc"
-DCMAKE_CXX_COMPILER="/opt/intel/bin/icpc" -DREGRESSIONTEST_DOWNLOAD=on

Hope it helps,
Luda

On Wed, Mar 25, 2020 at 4:46 AM Harry Mark Greenblatt <
harry.greenbl...@weizmann.ac.il> wrote:

> BS”D
>
> Dear All,
>
>  I would like to compile Gromacs 2020 with an intel compiler;  I set the
> following:
>
> -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on
> -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl
> -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include
>
> Despite the fact that I have told it to use the Intel C++ compile is
> (which it finds), it still looks and finds the system g++, which, of course
> is quite old.  If I have given it the name of a C++ compiler, why is it
> looking for g++?
>
>
>
> Thanks
>
> Harry
>
>
>
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology   harry.greenbl...@weizmann.ac.il
> 
> Weizmann Institute of SciencePhone:  972-8-934-6340
> 234 Herzl St.Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
>
> --
> 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.



-- 
Regards,

Lyudmyla Dorosh, PhD

University of Alberta
Department of Electrical and Computer Engineering,
4-030A ECERF
Edmonton, AB, T6G 2G8
Canada
Email: dor...@ualberta.ca
-- 
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[gmx-users] compile with intel compiler

[Harry Mark Greenblatt]

BS”D

Dear All,

 I would like to compile Gromacs 2020 with an intel compiler;  I set the 
following:

-DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on  
-DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl 
-DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include

Despite the fact that I have told it to use the Intel C++ compile is (which it 
finds), it still looks and finds the system g++, which, of course is quite old. 
 If I have given it the name of a C++ compiler, why is it looking for g++?



Thanks

Harry




Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel

-- 
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* Please search the archive at 
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