esys-escript

problem about numpy for install escript on ubuntu 18.04

Asked by mohammad kashkouli

Dear all,

I am trying to install escript on Ubuntu 18.04. I've used stretch_py3_mpi_options option for it. In addition, I used this script for install:

"scons -j1 options_file=/home/mohammad/Desktop/escript/python-escript_5.4/src/scons/templates/stretch_py3_mpi_options.py"

after that this error happend:
scons: Reading SConscript files ...
2.7.15rc1 (default, Nov 12 2018, 14:31:15)
[GCC 7.3.0]
Building with the following additional flags from debian: [['cpp_flags', '-Wdate-time -D_FORTIFY_SOURCE=2'], ['cxx_extra', '-g -O2 -fdebug-prefix-map=/home/mohammad/Desktop/escript/python-escript_5.4/src=. -fstack-protector-strong -Wformat -Werror=format-security'], ['ld_extra', '-Wl,-Bsymbolic-functions -Wl,-z,relro']]
Using options in /home/mohammad/Desktop/escript/python-escript_5.4/src/scons/templates/stretch_py3_mpi_options.py.
sh: 1: svnversion: not found
Using svn revision information from file. Got revision = 6851
Checking whether the C++ compiler works... yes
Checking for C++ function gethostname()... yes
Checking for C++ header file byteswap.h... yes
Checking for C++ function SCbswap32()... yes
Checking for C++ header file sys/endian.h... no
Checking for C++ header file libkern/OSByteOrder.h... no
Checking for working complex std::acos()... yes
Checking for C++ header file Python.h... yes
Checking for C++ function Py_Exit()... yes
Checking for C++ library boost_python-py36... yes
Checking for C++ library boost_python-py36... yes
Found boost/python/numpy.hpp. Building with boost numpy support.
Cannot import numpy. If it is installed try setting your PYTHONPATH and probably LD_LIBRARY_PATH

I tried to change python PATH to :

PYTHONPATH=/home/mohammad/Desktop/escript/python-escript_5.4/src

but same error happend. furthermore my LD library path is for intel compiler:

"LDLIBRARY="/opt/intel/lib"

How can I fix this issue?

Regards,
Mohammad

Question information

Language:
English Edit question
Status:
Solved
For:
esys-escript Edit question
Assignee:
No assignee Edit question
Solved by:
mohammad kashkouli
Solved:
Last query:
Last reply:
Revision history for this message
Adam Ellery (aellery) said : 		#1

Hi Mohammad,

Can you please confirm that you have numpy installed on your machine? You may need to run something like

sudo apt-get install python3-numpy

in the console before you run the scons command.

Best regards,

Adam

Revision history for this message
mohammad kashkouli (kashkoulimohammad) said : 		#2

Hi Adam,

Thanks for replying my question.
I had numpy on my machine and also checked it after this error.

mohammad@ubuntu:~/Desktop/escript/python-escript_5.4/src$ python
Python 2.7.15rc1 (default, Nov 12 2018, 14:31:15)
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> print numpy.__version__
1.16.2

Regards,

Mohammad

Revision history for this message
Adam Ellery (aellery) said : 		#3

Hi Mohammad,

You may have to install numpy a second time if you have both python 2.7 and python 3 installed on your computer, as Ubuntu has two separate numpy packages in the repository (one for each version of python.) Based on the output you posted, I believe that you may have python-numpy installed (the python 2.7 numpy module) but not python3-numpy.

Adam

Revision history for this message
mohammad kashkouli (kashkoulimohammad) said : 		#4

Hi Adam,

Thank you again.
Yes I have both of python and after I installed numpy on python3 the error solved but happened new error during build.

scons: *** [dummy] Error 255
scons: building terminated because of errors.

*** Config Summary (see config.log and <prefix>/lib/buildvars for details) ***
Escript revision 6851

  Install prefix: /home/mohammad/Desktop/escript/python-escript_5.4/src
          Python: python3 (Version 3.6.8)
           boost: /usr (Version 1.65.1)
        trilinos: NO
           numpy: YES (with headers)
             MPI: OPENMPI (Version 2.1.1)
            gmsh: YES, MPI-ENABLED
            gzip: YES
  Solver library: paso
   Direct solver: NONE
         domains: dudley, finley, ripley, speckley
          netcdf: YES (4 + 3)
           weipa: YES
          openmp: YES
            gdal: YES
          pyproj: YES
           scipy: YES
           sympy: YES

  DISABLED features: cppunit debug lapack mkl parmetis silo trilinos umfpack visit
  Treating warnings as errors

ERROR: build stopped due to errors

Regards,

Revision history for this message
Adam Ellery (aellery) said : 		#5

Hi Mohammad,

You may have another dependency that escript requires uninstalled. Could you please run the following commands:

sudo apt-get install python3-dev python3-numpy python3-pyproj python3-gdal python3-sympy python3-matplotlib python3-scipy libnetcdf-cxx-legacy-dev libnetcdf-c++4-dev libboost-random-dev libboost-python-dev scons lsb-release libsuitesparse-dev libopenmpi-dev

scons -j1 options_file=/home/mohammad/Desktop/escript/python-escript_5.4/src/scons/templates/stretch_py3_mpi_options.py

The first command will install all of the dependencies that escript requires, the second command will compile the code. Please tell me if you receive another error message.

Best regards,

Adam

Revision history for this message
mohammad kashkouli (kashkoulimohammad) said : 		#6

Hi Adam,

Thanks again for your consideration.
It is output for first command:

mohammad@ubuntu:~/Desktop/escript/python-escript_5.4/src$ sudo apt-get install python3-dev python3-numpy python3-pyproj python3-gdal python3-sympy python3-matplotlib python3-scipy libnetcdf-cxx-legacy-dev libnetcdf-c++4-dev libboost-random-dev libboost-python-dev scons lsb-release libsuitesparse-dev libopenmpi-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libsuitesparse-dev is already the newest version (1:5.1.2-2).
lsb-release is already the newest version (9.20170808ubuntu1).
python3-numpy is already the newest version (1:1.13.3-2ubuntu1).
libboost-python-dev is already the newest version (1.65.1.0ubuntu1).
libboost-random-dev is already the newest version (1.65.1.0ubuntu1).
libnetcdf-c++4-dev is already the newest version (4.3.0+ds-5).
libnetcdf-cxx-legacy-dev is already the newest version (4.2-8).
libopenmpi-dev is already the newest version (2.1.1-8).
libopenmpi-dev set to manually installed.
python3-matplotlib is already the newest version (2.1.1-2ubuntu3).
python3-scipy is already the newest version (0.19.1-2ubuntu1).
python3-sympy is already the newest version (1.1.1-5).
scons is already the newest version (3.0.1-1).
python3-dev is already the newest version (3.6.7-1~18.04).
python3-dev set to manually installed.
python3-gdal is already the newest version (2.4.2+dfsg-1~bionic0).
python3-pyproj is already the newest version (1.9.5.1-4~bionic0).
0 upgraded, 0 newly installed, 0 to remove and 465 not upgraded

All of dependency are installed but when I run second command same error happened.

Best Regards,
Mohammad

Revision history for this message
Adam Ellery (aellery) said : 		#7

Hi Mohammad,

Could you please post the text output that displays in the console just before the lines:

scons: *** [dummy] Error 255
scons: building terminated because of errors.

This should tell me more information about what your error is.

Best regards,
Adam

Revision history for this message
mohammad kashkouli (kashkoulimohammad) said : 		#8

For sure. These are all scripts:
mohammad@ubuntu:~/Desktop/escript/python-escript_5.4/src$ scons -j1 options_file=/home/mohammad/Desktop/escript/python-escript_5.4/src/scons/templates/stretch_py3_mpi_options.py
scons: Reading SConscript files ...
2.7.15rc1 (default, Nov 12 2018, 14:31:15)
[GCC 7.3.0]
Building with the following additional flags from debian: [['cpp_flags', '-Wdate-time -D_FORTIFY_SOURCE=2'], ['cxx_extra', '-g -O2 -fdebug-prefix-map=/home/mohammad/Desktop/escript/python-escript_5.4/src=. -fstack-protector-strong -Wformat -Werror=format-security'], ['ld_extra', '-Wl,-Bsymbolic-functions -Wl,-z,relro']]
Using options in /home/mohammad/Desktop/escript/python-escript_5.4/src/scons/templates/stretch_py3_mpi_options.py.
Using svn revision information from file. Got revision = 6851
Checking whether the C++ compiler works... (cached) yes
Checking for C++ function gethostname()... (cached) yes
Checking for C++ header file byteswap.h... (cached) yes
Checking for C++ function SCbswap32()... (cached) yes
Checking for C++ header file sys/endian.h... (cached) no
Checking for C++ header file libkern/OSByteOrder.h... (cached) no
Checking for working complex std::acos()... (cached) yes
Checking for C++ header file Python.h... (cached) yes
Checking for C++ function Py_Exit()... (cached) yes
Checking for C++ library boost_python-py36... (cached) yes
Checking for C++ library boost_python-py36... (cached) yes
Found boost/python/numpy.hpp. Building with boost numpy support.
Checking for C++ header file numpy/ndarrayobject.h... (cached) yes
Checking for C++ library netcdf_c++4... (cached) yes
Checking for C++ library mpi_cxx... yes
Checking for C++ library boost_iostreams... (cached) yes
Chmod("utest.sh", 0755)
Generated utest.sh.
Chmod("itest.sh", 0755)
Generated itest.sh.
Chmod("/home/mohammad/Desktop/escript/python-escript_5.4/src/bin/run-escript", 0755)
scons: done reading SConscript files.
scons: Building targets ...
Compiling build/posix/escriptcore/src/AbstractContinuousDomain.os
Compiling build/posix/escriptcore/src/AbstractDomain.os
Compiling build/posix/escriptcore/src/AbstractReducer.os
Compiling build/posix/escriptcore/src/AbstractSystemMatrix.os
Compiling build/posix/escriptcore/src/AbstractTransportProblem.os
Compiling build/posix/escriptcore/src/ArrayOps.os
Compiling build/posix/escriptcore/src/BinaryDataReadyOps.os
Compiling build/posix/escriptcore/src/Data.os
Compiling build/posix/escriptcore/src/DataAbstract.os
Compiling build/posix/escriptcore/src/DataConstant.os
Compiling build/posix/escriptcore/src/DataEmpty.os
Compiling build/posix/escriptcore/src/DataExpanded.os
Compiling build/posix/escriptcore/src/DataFactory.os
Compiling build/posix/escriptcore/src/DataLazy.os
Compiling build/posix/escriptcore/src/DataReady.os
Compiling build/posix/escriptcore/src/DataTagged.os
Compiling build/posix/escriptcore/src/DataTypes.os
Compiling build/posix/escriptcore/src/DataVector.os
Compiling build/posix/escriptcore/src/DataVectorAlt.os
Compiling build/posix/escriptcore/src/DataVectorOps.os
Compiling build/posix/escriptcore/src/DataVectorTaipan.os
Compiling build/posix/escriptcore/src/EscriptParams.os
Compiling build/posix/escriptcore/src/EsysMPI.os
Compiling build/posix/escriptcore/src/ExceptionTranslators.os
Compiling build/posix/escriptcore/src/FunctionSpace.os
Compiling build/posix/escriptcore/src/FunctionSpaceFactory.os
Compiling build/posix/escriptcore/src/MPIDataReducer.os
Compiling build/posix/escriptcore/src/MPIScalarReducer.os
Compiling build/posix/escriptcore/src/NonReducedVariable.os
Compiling build/posix/escriptcore/src/NullDomain.os
Compiling build/posix/escriptcore/src/Random.os
Compiling build/posix/escriptcore/src/SplitWorld.os
Compiling build/posix/escriptcore/src/SubWorld.os
Compiling build/posix/escriptcore/src/Taipan.os
Compiling build/posix/escriptcore/src/TestDomain.os
Compiling build/posix/escriptcore/src/Utils.os
Compiling build/posix/escriptcore/src/WrappedArray.os
Compiling build/posix/escriptcore/src/escriptcpp.os
Compiling build/posix/pythonMPI/ScriptMPI.o
Compiling build/posix/pythonMPI/ScriptMPIredirect.o
Compiling build/posix/paso/src/BiCGStab.os
Compiling build/posix/paso/src/Coupler.os
Compiling build/posix/paso/src/FCT_Solver.os
Compiling build/posix/paso/src/FluxLimiter.os
Compiling build/posix/paso/src/Functions.os
Compiling build/posix/paso/src/GMRES.os
Compiling build/posix/paso/src/GMRES2.os
Compiling build/posix/paso/src/MKL.os
Compiling build/posix/paso/src/NewtonGMRES.os
Compiling build/posix/paso/src/Options.os
Compiling build/posix/paso/src/PCG.os
Compiling build/posix/paso/src/PasoUtil.os
Compiling build/posix/paso/src/Pattern.os
Compiling build/posix/paso/src/Pattern_mis.os
Compiling build/posix/paso/src/Pattern_reduceBandwidth.os
Compiling build/posix/paso/src/Preconditioner.os
Compiling build/posix/paso/src/ReactiveSolver.os
Compiling build/posix/paso/src/SchurComplement.os
Compiling build/posix/paso/src/Smoother.os
Compiling build/posix/paso/src/Solver.os
Compiling build/posix/paso/src/Solver_Function.os
Compiling build/posix/paso/src/SparseMatrix.os
Compiling build/posix/paso/src/SparseMatrix_getSubmatrix.os
Compiling build/posix/paso/src/SparseMatrix_nullifyRowsAndCols.os
Compiling build/posix/paso/src/SparseMatrix_saveHB.os
Compiling build/posix/paso/src/SparseMatrix_MatrixMatrix.os
Compiling build/posix/paso/src/SparseMatrix_MatrixMatrixTranspose.os
Compiling build/posix/paso/src/SparseMatrix_MatrixVector.os
Compiling build/posix/paso/src/SystemMatrix.os
Compiling build/posix/paso/src/SystemMatrix_MatrixVector.os
Compiling build/posix/paso/src/SystemMatrix_copyRemoteCoupleBlock.os
Compiling build/posix/paso/src/SystemMatrix_debug.os
Compiling build/posix/paso/src/SystemMatrix_extendedRows.os
Compiling build/posix/paso/src/SystemMatrix_loadMM.os
Compiling build/posix/paso/src/SystemMatrix_mergeMainAndCouple.os
Compiling build/posix/paso/src/SystemMatrixPattern.os
Compiling build/posix/paso/src/SystemMatrixPattern_unrollBlocks.os
Compiling build/posix/paso/src/Transport.os
Compiling build/posix/paso/src/Transport_solve.os
Compiling build/posix/paso/src/ILU.os
Compiling build/posix/paso/src/MINRES.os
Compiling build/posix/paso/src/RILU.os
Compiling build/posix/paso/src/TFQMR.os
Compiling build/posix/paso/src/UMFPACK.os
Compiling build/posix/paso/src/performance.os
Compiling build/posix/paso/src/solve.os
Compiling build/posix/dudley/src/Assemble_AverageElementData.os
Compiling build/posix/dudley/src/Assemble_CopyElementData.os
Compiling build/posix/dudley/src/Assemble_CopyNodalData.os
Compiling build/posix/dudley/src/Assemble_LumpedSystem.os
Compiling build/posix/dudley/src/Assemble_NodeCoordinates.os
Compiling build/posix/dudley/src/Assemble_PDE.os
Compiling build/posix/dudley/src/Assemble_PDE_Points.os
Compiling build/posix/dudley/src/Assemble_PDE_Single_2D.os
Compiling build/posix/dudley/src/Assemble_PDE_Single_3D.os
Compiling build/posix/dudley/src/Assemble_PDE_System_2D.os
Compiling build/posix/dudley/src/Assemble_PDE_System_3D.os
Compiling build/posix/dudley/src/Assemble_addToSystemMatrix.os
Compiling build/posix/dudley/src/Assemble_getAssembleParameters.os
Compiling build/posix/dudley/src/Assemble_getNormal.os
Compiling build/posix/dudley/src/Assemble_getSize.os
Compiling build/posix/dudley/src/Assemble_integrate.os
Compiling build/posix/dudley/src/Assemble_interpolate.os
Compiling build/posix/dudley/src/DomainFactory.os
Compiling build/posix/dudley/src/DudleyDomain.os
Compiling build/posix/dudley/src/ElementFile.os
Compiling build/posix/dudley/src/ElementFile_createColoring.os
Compiling build/posix/dudley/src/ElementFile_distributeByRankOfDOF.os
Compiling build/posix/dudley/src/ElementFile_jacobians.os
Compiling build/posix/dudley/src/IndexList.os
Compiling build/posix/dudley/src/Mesh_distributeByRankOfDOF.os
Compiling build/posix/dudley/src/Mesh_getPattern.os
Compiling build/posix/dudley/src/Mesh_optimizeDOFDistribution.os
Compiling build/posix/dudley/src/Mesh_optimizeDOFLabeling.os
Compiling build/posix/dudley/src/Mesh_read.os
Compiling build/posix/dudley/src/Mesh_readGmsh.os
Compiling build/posix/dudley/src/Mesh_resolveNodeIds.os
Compiling build/posix/dudley/src/Mesh_tet4.os
Compiling build/posix/dudley/src/Mesh_tri3.os
Compiling build/posix/dudley/src/Mesh_write.os
Compiling build/posix/dudley/src/NodeFile.os
Compiling build/posix/dudley/src/NodeFile_createDenseLabelings.os
Compiling build/posix/dudley/src/NodeFile_createMappings.os
Compiling build/posix/dudley/src/NodeFile_createTrilinosGraph.os
Compiling build/posix/dudley/src/NodeFile_gather.os
Compiling build/posix/dudley/src/ShapeTable.os
Compiling build/posix/dudley/src/Util.os
Compiling build/posix/dudley/src/Assemble_gradient.os
Compiling build/posix/dudley/src/Assemble_jacobians.os
Compiling build/posix/dudley/src/dudleycpp.os
Compiling build/posix/finley/src/Assemble_AverageElementData.os
Compiling build/posix/finley/src/Assemble_CopyElementData.os
Compiling build/posix/finley/src/Assemble_CopyNodalData.os
Compiling build/posix/finley/src/Assemble_LumpedSystem.os
Compiling build/posix/finley/src/Assemble_NodeCoordinates.os
Compiling build/posix/finley/src/Assemble_PDE.os
Compiling build/posix/finley/src/Assemble_PDE_Points.os
Compiling build/posix/finley/src/Assemble_PDE_Single_1D.os
Compiling build/posix/finley/src/Assemble_PDE_Single_2D.os
Compiling build/posix/finley/src/Assemble_PDE_Single_3D.os
Compiling build/posix/finley/src/Assemble_PDE_Single_C.os
Compiling build/posix/finley/src/Assemble_PDE_System_1D.os
Compiling build/posix/finley/src/Assemble_PDE_System_2D.os
Compiling build/posix/finley/src/Assemble_PDE_System_3D.os
Compiling build/posix/finley/src/Assemble_PDE_System_C.os
Compiling build/posix/finley/src/Assemble_addToSystemMatrix.os
Compiling build/posix/finley/src/Assemble_getAssembleParameters.os
Compiling build/posix/finley/src/Assemble_getNormal.os
Compiling build/posix/finley/src/Assemble_getSize.os
Compiling build/posix/finley/src/Assemble_gradient.os
Compiling build/posix/finley/src/Assemble_integrate.os
Compiling build/posix/finley/src/Assemble_interpolate.os
Compiling build/posix/finley/src/Assemble_jacobians.os
Compiling build/posix/finley/src/DomainFactory.os
Compiling build/posix/finley/src/ElementFile.os
Compiling build/posix/finley/src/ElementFile_jacobians.os
Compiling build/posix/finley/src/FinleyDomain.os
Compiling build/posix/finley/src/IndexList.os
Compiling build/posix/finley/src/Mesh_addPoints.os
Compiling build/posix/finley/src/Mesh_findMatchingFaces.os
Compiling build/posix/finley/src/Mesh_getPasoPattern.os
Compiling build/posix/finley/src/Mesh_getTrilinosGraph.os
Compiling build/posix/finley/src/Mesh_glueFaces.os
Compiling build/posix/finley/src/Mesh_hex20.os
Compiling build/posix/finley/src/Mesh_hex8.os
Compiling build/posix/finley/src/Mesh_joinFaces.os
Compiling build/posix/finley/src/Mesh_merge.os
Compiling build/posix/finley/src/Mesh_optimizeDOFDistribution.os
Compiling build/posix/finley/src/Mesh_read.os
Compiling build/posix/finley/src/Mesh_readGmsh.os
Compiling build/posix/finley/src/Mesh_rec4.os
Compiling build/posix/finley/src/Mesh_rec8.os
Compiling build/posix/finley/src/Mesh_write.os
Compiling build/posix/finley/src/NodeFile.os
Compiling build/posix/finley/src/Quadrature.os
Compiling build/posix/finley/src/ReferenceElements.os
Compiling build/posix/finley/src/ShapeFunctions.os
Compiling build/posix/finley/src/Util.os
Compiling build/posix/finley/src/finleycpp.os
Compiling build/posix/ripley/src/blocktools.os
Compiling build/posix/ripley/src/blocktools2.os
Compiling build/posix/ripley/src/Brick.os
Compiling build/posix/ripley/src/DefaultAssembler2D.os
Compiling build/posix/ripley/src/DefaultAssembler3D.os
Compiling build/posix/ripley/src/domainhelpers.os
Compiling build/posix/ripley/src/LameAssembler2D.os
Compiling build/posix/ripley/src/LameAssembler3D.os
Compiling build/posix/ripley/src/MultiBrick.os
Compiling build/posix/ripley/src/MultiRectangle.os
Compiling build/posix/ripley/src/Rectangle.os
Compiling build/posix/ripley/src/RipleyDomain.os
Compiling build/posix/ripley/src/WaveAssembler2D.os
Compiling build/posix/ripley/src/WaveAssembler3D.os
Compiling build/posix/ripley/src/ripleycpp.os
Compiling build/posix/speckley/src/AbstractAssembler.os
Compiling build/posix/speckley/src/Brick.os
Compiling build/posix/speckley/src/BrickGradients.os
Compiling build/posix/speckley/src/BrickIntegrals.os
Compiling build/posix/speckley/src/BrickReductions.os
Compiling build/posix/speckley/src/DefaultAssembler2D.os
Compiling build/posix/speckley/src/DefaultAssembler3D.os
Compiling build/posix/speckley/src/domainhelpers.os
Compiling build/posix/speckley/src/Rectangle.os
Compiling build/posix/speckley/src/RectangleGradients.os
Compiling build/posix/speckley/src/RectangleIntegrals.os
Compiling build/posix/speckley/src/RectangleReductions.os
Compiling build/posix/speckley/src/SpeckleyDomain.os
Compiling build/posix/speckley/src/WaveAssembler2D.os
Compiling build/posix/speckley/src/WaveAssembler3D.os
Compiling build/posix/speckley/src/CrossDomainCoupler.os
Compiling build/posix/speckley/src/speckleycpp.os
Compiling build/posix/weipa/src/DataVar.os
Compiling build/posix/weipa/src/EscriptDataset.os
Compiling build/posix/weipa/src/FinleyDomain.os
Compiling build/posix/weipa/src/FinleyElements.os
Compiling build/posix/weipa/src/FinleyNodes.os
Compiling build/posix/weipa/src/RipleyDomain.os
Compiling build/posix/weipa/src/RipleyElements.os
Compiling build/posix/weipa/src/RipleyNodes.os
Compiling build/posix/weipa/src/SpeckleyDomain.os
Compiling build/posix/weipa/src/SpeckleyElements.os
Compiling build/posix/weipa/src/SpeckleyNodes.os
Compiling build/posix/weipa/src/VisItControl.os
Compiling build/posix/weipa/src/weipacpp.os
python3 scripts/py_comp.py weipa/py_src/__init__.py build/posix/weipa/py/__init__.pyc
Compiling build/posix/weipa/src/reader_DataVar.os
Compiling build/posix/weipa/src/reader_EscriptDataset.os
Compiling build/posix/weipa/src/reader_FinleyDomain.os
Compiling build/posix/weipa/src/reader_FinleyElements.os
Compiling build/posix/weipa/src/reader_FinleyNodes.os
/home/mohammad/Desktop/escript/python-escript_5.4/src/bin/run-escript /home/mohammad/Desktop/escript/python-escript_5.4/src/build/scripts/release_sanity.py
[mpiexec@ubuntu] match_arg (../../utils/args/args.c:254): unrecognized argument gmca
[mpiexec@ubuntu] HYDU_parse_array (../../utils/args/args.c:269): argument matching returned error
[mpiexec@ubuntu] parse_args (../../ui/mpich/utils.c:4770): error parsing input array
[mpiexec@ubuntu] HYD_uii_mpx_get_parameters (../../ui/mpich/utils.c:5106): unable to parse user arguments

Usage: ./mpiexec [global opts] [exec1 local opts] : [exec2 local opts] : ...

Global options (passed to all executables):

  Global environment options:
    -genv {name} {value} environment variable name and value
    -genvlist {env1,env2,...} environment variable list to pass
    -genvnone do not pass any environment variables
    -genvall pass all environment variables not managed
                                          by the launcher (default)

  Other global options:
    -f {name} | -hostfile {name} file containing the host names
    -hosts {host list} comma separated host list
    -configfile {name} config file containing MPMD launch options
    -machine {name} | -machinefile {name}
                                     file mapping procs to machines
    -pmi-connect {nocache|lazy-cache|cache}
                                     set the PMI connections mode to use
    -pmi-aggregate aggregate PMI messages
    -pmi-noaggregate do not aggregate PMI messages
    -trace {<libraryname>} trace the application using <libraryname>
                                     profiling library; default is libVT.so
    -trace-imbalance {<libraryname>} trace the application using <libraryname>
                                     imbalance profiling library; default is libVTim.so
    -check-mpi {<libraryname>} check the application using <libraryname>
                                     checking library; default is libVTmc.so
    -ilp64 Preload ilp64 wrapper library for support default size of
                                     integer 8 bytes
    -mps start statistics gathering for MPI Performance Snapshot (MPS)
    -aps start statistics gathering for Application Performance Snapshot (APS)
    -trace-pt2pt collect information about
                                     Point to Point operations
    -trace-collectives collect information about
                                     Collective operations
    -tune [<confname>] apply the tuned data produced by
                                     the MPI Tuner utility
    -use-app-topology <statfile> perform optimized rank placement based statistics
                                     and cluster topology
    -noconf do not use any mpiexec's configuration files
    -branch-count {leaves_num} set the number of children in tree
    -gwdir {dirname} working directory to use
    -gpath {dirname} path to executable to use
    -gumask {umask} mask to perform umask
    -tmpdir {tmpdir} temporary directory for cleanup input file
    -cleanup create input file for clean up
    -gtool {options} apply a tool over the mpi application
    -gtoolfile {file} apply a tool over the mpi application. Parameters specified in the file

Local options (passed to individual executables):

  Local environment options:
    -env {name} {value} environment variable name and value
    -envlist {env1,env2,...} environment variable list to pass
    -envnone do not pass any environment variables
    -envall pass all environment variables (default)

  Other local options:
    -host {hostname} host on which processes are to be run
    -hostos {OS name} operating system on particular host
    -wdir {dirname} working directory to use
    -path {dirname} path to executable to use
    -umask {umask} mask to perform umask
    -n/-np {value} number of processes
    {exec_name} {args} executable name and arguments

Hydra specific options (treated as global):

  Bootstrap options:
    -bootstrap bootstrap server to use
     (ssh rsh pdsh fork slurm srun ll llspawn.stdio lsf blaunch sge qrsh persist service pbsdsh)
    -bootstrap-exec executable to use to bootstrap processes
    -bootstrap-exec-args additional options to pass to bootstrap server
    -prefork use pre-fork processes startup method
    -enable-x/-disable-x enable or disable X forwarding

  Resource management kernel options:
    -rmk resource management kernel to use (user slurm srun ll llspawn.stdio lsf blaunch sge qrsh pbs cobalt)

  Processor topology options:
    -binding process-to-core binding mode
  Extended fabric control options:
    -rdma select RDMA-capable network fabric (dapl). Fallback list is ofa,tcp,tmi,ofi
    -RDMA select RDMA-capable network fabric (dapl). Fallback is ofa
    -dapl select DAPL-capable network fabric. Fallback list is tcp,tmi,ofa,ofi
    -DAPL select DAPL-capable network fabric. No fallback fabric is used
    -ib select OFA-capable network fabric. Fallback list is dapl,tcp,tmi,ofi
    -IB select OFA-capable network fabric. No fallback fabric is used
    -tmi select TMI-capable network fabric. Fallback list is dapl,tcp,ofa,ofi
    -TMI select TMI-capable network fabric. No fallback fabric is used
    -mx select Myrinet MX* network fabric. Fallback list is dapl,tcp,ofa,ofi
    -MX select Myrinet MX* network fabric. No fallback fabric is used
    -psm select PSM-capable network fabric. Fallback list is dapl,tcp,ofa,ofi
    -PSM select PSM-capable network fabric. No fallback fabric is used
    -psm2 select Intel* Omni-Path Fabric. Fallback list is dapl,tcp,ofa,ofi
    -PSM2 select Intel* Omni-Path Fabric. No fallback fabric is used
    -ofi select OFI-capable network fabric. Fallback list is tmi,dapl,tcp,ofa
    -OFI select OFI-capable network fabric. No fallback fabric is used

  Checkpoint/Restart options:
    -ckpoint {on|off} enable/disable checkpoints for this run
    -ckpoint-interval checkpoint interval
    -ckpoint-prefix destination for checkpoint files (stable storage, typically a cluster-wide file system)
    -ckpoint-tmp-prefix temporary/fast/local storage to speed up checkpoints
    -ckpoint-preserve number of checkpoints to keep (default: 1, i.e. keep only last checkpoint)
    -ckpointlib checkpointing library (blcr)
    -ckpoint-logfile checkpoint activity/status log file (appended)
    -restart restart previously checkpointed application
    -ckpoint-num checkpoint number to restart

  Demux engine options:
    -demux demux engine (poll select)

  Debugger support options:
    -tv run processes under TotalView
    -tva {pid} attach existing mpiexec process to TotalView
    -gdb run processes under GDB
    -gdba {pid} attach existing mpiexec process to GDB
    -gdb-ia run processes under Intel IA specific GDB

  Other Hydra options:
    -v | -verbose verbose mode
    -V | -version show the version
    -info build information
    -print-rank-map print rank mapping
    -print-all-exitcodes print exit codes of all processes
    -iface network interface to use
    -help show this message
    -perhost <n> place consecutive <n> processes on each host
    -ppn <n> stand for "process per node"; an alias to -perhost <n>
    -grr <n> stand for "group round robin"; an alias to -perhost <n>
    -rr involve "round robin" startup scheme
    -s <spec> redirect stdin to all or 1,2 or 2-4,6 MPI processes (0 by default)
    -ordered-output avoid data output intermingling
    -profile turn on internal profiling
    -l | -prepend-rank prepend rank to output
    -prepend-pattern prepend pattern to output
    -outfile-pattern direct stdout to file
    -errfile-pattern direct stderr to file
    -localhost local hostname for the launching node
    -nolocal avoid running the application processes on the node where mpiexec.hydra started

Intel(R) MPI Library for Linux* OS, Version 2018 Update 3 Build 20180411 (id: 18329)
Copyright 2003-2018 Intel Corporation.
scons: *** [dummy] Error 255
scons: building terminated because of errors.

*** Config Summary (see config.log and <prefix>/lib/buildvars for details) ***
Escript revision 6851

  Install prefix: /home/mohammad/Desktop/escript/python-escript_5.4/src
          Python: python3 (Version 3.6.8)
           boost: /usr (Version 1.65.1)
        trilinos: NO
           numpy: YES (with headers)
             MPI: OPENMPI (Version 2.1.1)
            gmsh: YES, MPI-ENABLED
            gzip: YES
  Solver library: paso
   Direct solver: NONE
         domains: dudley, finley, ripley, speckley
          netcdf: YES (4 + 3)
           weipa: YES
          openmp: YES
            gdal: YES
          pyproj: YES
           scipy: YES
           sympy: YES

  DISABLED features: cppunit debug lapack mkl parmetis silo trilinos umfpack visit
  Treating warnings as errors

ERROR: build stopped due to errors

Regards,
Mohammad

Revision history for this message
Adam Ellery (aellery) said : 		#9

Hi Mohammad,

I think we've nearly got it working. Can you please run:

scons -j1 options_file=/home/mohammad/Desktop/escript/python-escript_5.4/src/scons/templates/stretch_py3_options.py mpi="MPICH2"

Best regards,

Adam

Revision history for this message
mohammad kashkouli (kashkoulimohammad) said : 		#10

Hi Adam,

Thanks again.
The Escript build is completed successfully.

/home/mohammad/Desktop/escript/python-escript_5.4/src/bin/run-escript /home/mohammad/Desktop/escript/python-escript_5.4/src/build/scripts/release_sanity.py
/home/mohammad/Desktop/escript/python-escript_5.4/src/bin/run-escript: 479: /home/mohammad/Desktop/escript/python-escript_5.4/src/bin/run-escript: mpdboot: not found
/home/mohammad/Desktop/escript/python-escript_5.4/src/bin/run-escript: 484: /home/mohammad/Desktop/escript/python-escript_5.4/src/bin/run-escript: mpdallexit: not found
scons: done building targets.

*** Config Summary (see config.log and <prefix>/lib/buildvars for details) ***
Escript revision 6851

  Install prefix: /home/mohammad/Desktop/escript/python-escript_5.4/src
          Python: python3 (Version 3.6.8)
           boost: /usr (Version 1.65.1)
        trilinos: NO
           numpy: YES (with headers)
             MPI: YES (flavour: MPICH2)
            gmsh: YES, MPI-ENABLED
            gzip: YES
  Solver library: paso
   Direct solver: NONE
         domains: dudley, finley, ripley, speckley
          netcdf: YES (4 + 3)
           weipa: YES
          openmp: YES
            gdal: YES
          pyproj: YES
           scipy: YES
           sympy: YES

  DISABLED features: cppunit debug lapack mkl parmetis silo trilinos umfpack visit
  Treating warnings as errors

SUCCESS: build complete

Best Regards,
Mohammad