ICC-MPI comiple failed

[Albert]

Hello:

I am trying to compile plumed-2.02 with intel ICC+intel MPI, but it failed with messages:

cd plumed-2.0.2/

export plumeddir="/home/albert/install/plumed-2.0.2"

export PLUMED_ROOT="/home/albert/install/plumed-2.0.2"

export PLUMED_PREFIX="/home/albert/install/plumed-2.0.2"

./configure.sh 

1) linux.gcc               4) linux.mpi.icc

2) linux.icc               5) linux.xcompile.mingw32

3) linux.mpi.gcc

Choose a configuration: 4

source sourceme.sh 

make

--------------------log----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

make[6]: Entering directory `/home/albert/install/plumed-2.0.2/src/analysis'

mpic++ -c -MM -MFHistogram.d -D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI  -I.   -O -fPIC -Wall -wd981,383,1418 Histogram.cpp

g++: error: unrecognized command line option ‘-wd981,383,1418’

make[6]: *** [Histogram.o] Error 1

make[6]: Leaving directory `/home/albert/install/plumed-2.0.2/src/analysis'

make[5]: *** [../analysis] Error 2

make[5]: Leaving directory `/home/albert/install/plumed-2.0.2/src/lib'

make[4]: *** [dirs] Error 2

make[4]: Leaving directory `/home/albert/install/plumed-2.0.2/src/lib'

make[3]: *** [all] Error 2

make[3]: Leaving directory `/home/albert/install/plumed-2.0.2/src/lib'

make[2]: *** [lib] Error 2

make[2]: Leaving directory `/home/albert/install/plumed-2.0.2/src'

make[1]: *** [lib] Error 2

make[1]: Leaving directory `/home/albert/install/plumed-2.0.2'

make: *** [all] Error 2

--------------------log----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

it is really strange that I choose icc-mpi, why it claimed g++ there? It looks like compile it with gcc instead of intel icc?

thx a lot

Albert

[Giovanni Bussi]

It seems that on your machine mpic++ is not the intel compiler but gcc. 

You should use the configuration file for gcc or make sure that mpic++ is the intel compiler. Alternatively, edit the Makefile.conf file setting the name of the intel mpi compiler.

Giovanni

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[Albert]

Hi Giovanni:

thanks again for kind helps.

The problem solved now after I modified Makefile.conf . However, it has another claimed

make[6]: Entering directory `/home/albert/install/plumed-2.0.2/src/analysis'

icpc -c -MM -MFAnalysis.d -D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI  -I.   -O -fPIC -Wall -wd981,383,1418 Analysis.cpp

core/../../core/tools/../../tools/Communicator.h(25): catastrophic error: cannot open source file "mpi.h"

  #include <mpi.h>

                  ^

make[6]: *** [Analysis.o] Error 4

make[6]: Leaving directory `/home/albert/install/plumed-2.0.2/src/analysis'

make[5]: *** [../analysis] Error 2

It seems that it cannot find mpi.h file. I checked in my intel diretory, it is there:

install/plumed-2.0.2> find /opt/intel/ -name 'mpi.h'

/opt/intel/impi/4.1.3.049/mic/include/mpi.h

/opt/intel/impi/4.1.3.049/ia32/include/mpi.h

/opt/intel/impi/4.1.3.049/intel64/include/mpi.h

在 2014年5月14日星期三UTC+2下午6时08分34秒，Giovanni Bussi写道：

[Giovanni Bussi]

You are trying to use "icpc", which is not a mpi compiler.

I think you first have to decide which compiler you will use and understand:

1. if it supports mpi

2. if it is gnu or intel.

It would help if you first try to compile gromacs, then look at what compiler is used.

Giovanni

[Albert]

Intel MPI doesn't contains program called mpic++, so I modified it into icpc. Here is the full list for what I get for intel ICC and MPI:


codecov           compilervars.sh  icc   idb   ifort          inspxe-runsc  link_install.sh  profdcg    proforder      tselect  xild
compilervars.csh  fpp              icpc  idbc  inspxe-inject  inspxe-wrap   map_opts         profmerge  sourcechecker  xiar



compchk.sh        mpdallexit.py   mpdcleanup     mpdhelp.py      mpdman.py       mpdrun.py     mpicleanup     mpif90   mpiifort     pmi_proxy
cpuinfo           mpdboot         mpdcleanup.py  mpdkilljob      mpd.py          mpdsigjob     mpicxx         mpifc    mpirun       tune
hydra_nameserver  mpdboot.py      mpdexit        mpdkilljob.py   mpdringtest     mpdsigjob.py  mpiexec        mpigcc   mpitune
IMB-MPI1          mpdcheck        mpdexit.py     mpdlib.py       mpdringtest.py  mpdtrace      mpiexec.hydra  mpigxx   mpivars.csh
mpd               mpdcheck.py     mpdgdbdrv.py   mpdlistjobs     mpdroot         mpdtrace.py   mpiexec.py     mpiicc   mpivars.sh
mpdallexit        mpdchkpyver.py  mpdhelp        mpdlistjobs.py  mpdrun          mpicc         mpif77         mpiicpc  mtv.so




I can installed Gromacs with intel ICC+ intel MPI without any problem, and I can run jobs well.

I decided to use intel compile with mpi for plumed patched Gromacs.


do you have any idea how to solve the problem? It seems that my current problem is make plumed-2.0 knows how to find the "mpi.h" file in intel compiler directory.

thx a lot


在 2014年5月14日星期三UTC+2下午6时45分37秒，Giovanni Bussi写道：

[Giovanni Bussi]

I think your MPI installation is gcc based, so you either have to reconfigure MPI to use intel compiler or use it with gcc. 

Inviato da iPhone

[Massimiliano Bonomi]

mpicxx should be the C++ mpi compiler

Max

Sent from my iPhone. Please excuse typos and brevity.

[Albert]

thanks a lot.

problem solved after I compile openMPI with icc.

thanks again for kind helps.

Albert




在 2014年5月14日星期三UTC+2下午8时43分06秒，Giovanni Bussi写道：

[Albert]

Maybe.

But I found there are still some problem if I try to use mpicxx from intel compiler directly. It seems that it will have some problem to use intel MPI directly.....



------------Makefile.conf------------------
LIBS=-ldl
DYNAMIC_LIBS=-lstdc++ -llapack -lblas
DOUBLEPRECISION=-r8

CPPFLAGS=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE)
CXXFLAGS=-O -fPIC -Wall -wd981,383,1418
CFLAGS=-O -fPIC -Wall

LDFLAGS=-rdynamic
SOEXT=so
LDSO=mpicc -shared $(CFLAGS)
LD=mpicxx
LDF90=mpif90
CXX=mpicxx
CC=mpicc
FC=mpif90

GCCDEP=mpicxx
------------Makefile.conf------------------



make[6]: Entering directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src/colvar'
mpicxx -c -MM -MFTorsion.d -D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI  -I.   -O -fPIC -Wall -wd981,383,1418 Torsion.cpp

g++: error: unrecognized command line option ‘-wd981,383,1418’

make[6]: *** [Value.o] Error 1
make[6]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src/bias'
make[5]: *** [../bias] Error 2
make[5]: *** Waiting for unfinished jobs....
mpicxx -c -MM -MFAnalysis.d -D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI  -I.   -O -fPIC -Wall -wd981,383,1418 Analysis.cpp

g++: error: unrecognized command line option ‘-wd981,383,1418’
make[6]: *** [Histogram.o] Error 1

make[6]: *** Waiting for unfinished jobs....mpicxx -c -MM -MFSumHills.d -D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI  -I.   -O -fPIC -Wall -wd981,383,1418 SumHills.cpp

g++: error: unrecognized command line option ‘-wd981,383,1418’

make[6]: g++: error: unrecognized command line option ‘-wd981,383,1418’
*** [Manual.o] Error 1
make[6]: *** Waiting for unfinished jobs....
mpicxx -c -MM -MFCoordination.d -D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI  -I.   -O -fPIC -Wall -wd981,383,1418 Coordination.cpp
make[6]: *** [Torsion.o] Error 1
make[6]: *** Waiting for unfinished jobs....

g++: error: unrecognized command line option ‘-wd981,383,1418’

make[6]: *** [Analysis.o] Error 1
make[6]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src/analysis'

make[5]: *** [../analysis] Error 2

g++: error: unrecognized command line option ‘-wd981,383,1418’

make[6]: *** [SumHills.o] Error 1
make[6]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src/cltools'
make[5]: *** [../cltools] Error 2

g++: error: unrecognized command line option ‘-wd981,383,1418’

make[6]: *** [Coordination.o] Error 1
make[6]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src/colvar'
make[5]: *** [../colvar] Error 2
make[5]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src/lib'

make[4]: *** [dirs] Error 2

make[4]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src/lib'

make[3]: *** [all] Error 2

make[3]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src/lib'

make[2]: *** [lib] Error 2

make[2]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2/src'

make[1]: *** [lib] Error 2

make[1]: Leaving directory `/home/albert/Downloads/gromacs/plumed-2.0.2'

make: *** [all] Error 2

在 2014年5月14日星期三UTC+2下午8时50分18秒，Max写道：

[Carlo Camilloni]

it looks like your mpicxx is linked to g++ instead of icpc.

this depend on how your computer is configured,

alternatively you can check whether you have

mpiicpc

and

mpiicc

or you can try to export 

export I_MPI_CC=icc

export I_MPI_CXX=icpc

before starting the compilation.

Carlo

[Carlo Camilloni]

Hi,

if you add to CPPFLAGS:

-DMPICH_IGNORE_CXX_SEEK

it will work

Carlo

On 14 May 2014, at 22:03, yua...@gmail.com wrote:

Hello Carlo:

thanks a lot for the kind messages. Here is my new Makefile.conf:

LIBS=-ldl
DYNAMIC_LIBS=-lstdicpc -llapack -lblas

DOUBLEPRECISION=-r8

CPPFLAGS=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE)
CXXFLAGS=-O -fPIC -Wall -wd981,383,1418
CFLAGS=-O -fPIC -Wall

LDFLAGS=-rdynamic
SOEXT=so

LDSO=mpiicc -shared $(CFLAGS)
LD=mpiicpc
LDF90=mpif90
CXX=mpiicpc
CC=mpiicc
FC=mpif90

GCCDEP=mpiicpc


I have both mpiicpc and mpicc, but it still failed:


home/albert/install/intel-2013update4/impi/intel64/include/mpicxx.h(95): catastrophic error: #error directive: "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
  #error "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
   ^
make[6]: *** [MetaD.o] Error 4

make[6]: *** Waiting for unfinished jobs....

mpiicpc -c -D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI  -I.   -O -fPIC -Wall -wd981,383,1418 UWalls.cpp -o UWalls.o

On Wednesday, May 14, 2014 9:16:12 PM UTC+2, Carlo Camilloni wrote:

it looks like your mpicxx is linked to g++ instead of icpc.

this depend on how your computer is configured,

alternatively you can check whether you have

mpiicpc

and

mpiicc

or you can try to export 

export I_MPI_CC=icc

export I_MPI_CXX=icpc

before starting the compilation.

Carlo

[Albert]

Hi Carlo:

thanks for such useful advices. the "make" step finished without any errors.

but there is some errors for "make install"

cd ../../ ; tar cf - patches scripts src/*/*.h src/*/*.cpp src/*/*.o src/config/compile_options.sh *-doc | tar xf - -C /home/albert/install/plumed-2.0.2/lib/plumed-/home/albert/install/plumed-2.0.2//
cd ../../src ; tar cf - */*.h $(find . -type l) | tar xf - -C /home/albert/install/plumed-2.0.2/include/plumed-/home/albert/install/plumed-2.0.2/
for file in Plumed.inc* Plumed.cmake* ; do sed "s| /home/albert/install/plumed-2.0.2/source| /home/albert/install/plumed-2.0.2/lib/plumed-/home/albert/install/plumed-2.0.2//|g" $file > /home/albert/install/plumed-2.0.2/lib/plumed-/home/albert/install/plumed-2.0.2//src/lib/$file ; done
ln -s /home/albert/install/plumed-2.0.2/lib/plumed-/home/albert/install/plumed-2.0.2//src/lib/plumed /home/albert/install/plumed-2.0.2/bin/plumed-/home/albert/install/plumed-2.0.2
ln: failed to create symbolic link ‘/home/albert/install/plumed-2.0.2/bin/plumed-/home/albert/install/plumed-2.0.2’: No such file or directory
make[3]: *** [install-do] Error 1
make[3]: Leaving directory `/home/albert/install/plumed-2.0.2/source/src/lib'
make[2]: *** [install] Error 2
make[2]: Leaving directory `/home/albert/install/plumed-2.0.2/source/src/lib'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/albert/install/plumed-2.0.2/source/src'
make: *** [install] Error 2


here is my environment setting before compiling:

export plumeddir=/home/albert/install/plumed-2.0.2/source
export PLUMED_ROOT=/home/albert/install/plumed-2.0.2/source
export PLUMED_ROOT=/home/albert/install/plumed-2.0.2/source
export PLUMED_PREFIX=/home/albert/install/plumed-2.0.2

thanks again

在 2014年5月14日星期三UTC+2下午10时23分08秒，Carlo Camilloni写道：

[Giovanni Bussi]

Hi Albert,

it looks that also PLUMED_LIBSUFFIX is defined. Could you double check the environment?

env | grep PLUMED_

See this page for instructions on the environment variables for installation: http://plumed.github.io/doc-v2.0/user-doc/html/_installation.html

Ciao!

Giovanni