Install Mpich Cygwin
I am trying to setup cygwin and openmpi on windows. I have cygwin and I selected the openmpi packages from cygwin installer but it seems that when I try to compile my programs using mpicc the compiler seems to not be able to see mpicc. I have in my path the path to my cygwin bin. Update: Below is the error message when using command mpicc -o bpmain2 bpmain2.c Program 'mpicc' failed to run: No application is associated with the specified file for this operationAt line:1 char:1 + mpicc -o bpmain2 bpmain2.c +. At line:1 char:1 + mpicc -o bpmain2 bpmain2.c + + CategoryInfo: ResourceUnavailable: (:) , ApplicationFailedException + FullyQualifiedErrorId: NativeCommandFailed.
Quick Instructions:. On systems where MPI and BLAS/LAPACK are installed./configure. make all test. Or to specify compilers and have PETSc download and install MPI and BLAS/LAPACK (when they are not already on your machine)./configure -with-cc=gcc -with-cxx=g -with-fc=gfortran -download-mpich -download-fblaslapack. make all test Encounter problems?. Read the error message from./configure! I.
make problems? Just copy/paste make command printed by configure including PETSCDIR and PETSCARCH options. Do not have fortran compiler? Check below. Check the section Notes:. Please the latest patched tarball. We highly recommend installing PETSc as a regular/non-root user, perhaps in /home/username/soft.
To extract the sources use: gunzip -c petsc-3.8.0.tar.gz tar -xof -. Please check:./configure -help. Please check. To install in and for. and. Examples are at config/examples/.py.
We use some of these scripts locally for testing - for example one can update these files and run as:./config/examples/arch-osx-10.6.py. Assuming BLAS, LAPACK, MPICH are not currently installed./configure will download & install BLAS, LAPACK, MPICH if they are not already installed on the system):./configure -with-cc=gcc -with-cxx=g -with-fc=gfortran -download-fblaslapack -download-mpich. Same as above - but do not have a fortran compiler and want to use PETSc from C only./configure -with-cc=gcc -with-cxx=0 -with-fc=0 -download-f2cblaslapack -download-mpich. If BLAS, LAPACK, MPI sources (in '-devel' packages in most distros) are already installed in default system/compiler locations and mpicc, mpif90, mpiexec are available via PATH - configure does not require any additional options.
Compile and use MPICH instead! During installation of cygwin you need to add these extra packages. //github.com/CFDEMproject/LIGGGHTS-PUBLIC.git liggghts. > Did you get any errors during the MPICH2 install process (using the windows installers)? It's my fault. >>> Fatal Error: File 'mpi.mod' opened at (1) is not a GFORTRAN module file > The fortran module file provided with MPICH2 on Windows (binaries installed using windows installer) is only compatible with Intel Fortran Compiler for Windows. Attempting to compile MPICH2 on a Windows machine using Cygwin. A bit of relevant information $ uname -> CYGWIN_NT-6.1 $ gcc --version -> gcc (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.125) Copyright (C) 2004 Free Software Foundation, Inc. This is free software; see the source for copying conditions.
Specify compilers and compiler options used to build PETSc and perhaps external packages. Specify compilers using the options -with-cc -with-cxx -with-fc for c, c, and fortran compilers.with-cc=mpicc -with-cxx=mpicxx -with-fc=mpif90.with-cc=gcc -with-cxx=g -with-fc=gfortran.with-cc=gcc -with-cxx=g -with-fc=gfortran -with-clanguage=cxx Note that -with-clanguage=cxx means that the PETSc source code is compiled with the C compiler. This is not normally needed and we don't recommend it. One can use 'c' build of PETSc from both C and C. One can also have a complex build with C99.
If fortran compiler is not available or not needed - then disabling using fortran.with-fc=0. If a C compiler is not available or not needed - disable configuring with it.with-cxx=0. If no compilers are specified - configure will automatically look for available MPI or regular compilers in the user's PATH.
mpicc/mpiCC/mpif90 or mpif77. gcc/g/gfortran or g77. cc/CC/f77 etc. It's best to use MPI compilers as this will avoid the situation where MPI is compiled with one set of compilers like gcc/g77 and user specified incompatible compilers to PETSc perhaps icc/ifort.
This can be done by either specifying -with-cc=mpicc or -with-mpi-dir and not -with-cc=gcc.with-cc=mpicc -with-cxx=mpicxx -with-fc=mpif90.with-mpi-dir=/opt/mpich2-1.1 but.no.with-cc=gcc. Configure defaults to building PETSc in debug mode.
One can switch to using optimzed mode with the toggle option -with-debugging defaults to debug enabled. Additionally one can specify more suitable optimization flags with the options COPTFLAGS, FOPTFLAGS, CXXOPTFLAGS. For ex: when using gnu compilers with corresponding optimization flags:./configure -with-cc=gcc -with-cxx=g -with-fc=gfortran -with-debugging=0 COPTFLAGS='-O3 -march=native -mtune=native' CXXOPTFLAGS='-O3 -march=native -mtune=native' FOPTFLAGS='-O3 -march=native -mtune=native' -download-mpich. Configure cannot detect compiler libraries for certain set of compilers. In this case one can specify additional system/compiler libraries using the LIBS option./configure -LIBS='-ldl /usr/lib/libm.a'.
These packages provide some basic numeric kernels used by PETSc. Configure will automatically look for blas/lapack in certain standard locations, on most systems you should not need to provide any information about BLAS/LAPACK in the./configure command. One can use the following options to let configure download/install blas/lapack automatically.download-fblaslapack when fortran compiler is present.download-f2cblaslapack when configuring without a fortran compiler - i.e -with-fc=0. Alternatively one can use other options like one of the following.with-blaslapack-lib=libsunperf.a.with-blas-lib=libblas.a -with-lapack-lib=liblapack.a.with-blaslapack-dir=/soft/com/packages/intel/13/079/mkl Notes:. Intel MKL Intel provides blas/lapack via library. It usually works from GNU/Intel compilers on linux and MS/Intel compilers on Windows. One can specify it to PETSc configure with for eg: -with-blaslapack-dir=/soft/com/packages/intel/13/079/mkl If the above option does not work - one could determine the correct library list for your compilers using and specify with the configure option -with-blaslapack-lib.
IBM ESSL Sadly, IBM's ESSL does not have all the routines of BLAS and LAPACK that some packages, such as SuperLU expect; in particular slamch, dlamch and xerbla. In this case instead of using ESSL we suggest -download-fblaslapack.
If you really want to use ESSL, see. This software provides the parallel functionality for PETSc. Configure will automatically look for MPI compilers mpicc/mpif77 etc and use them if found in your PATH. One can use the following options to let configure download/install MPI automatically.download-mpich install and use MPICH.download-openmpi Install and use Open MPI. See for other installation options.
It's best to install PETSc with MPI compiler wrappers (often called mpicc, mpicxx, mpif90) - this way, the SAME compilers used to build MPI are used to build PETSc this avoids incompatibilities which might crop up - when using libraries compiled with different c or fortran compilers. This can be achieved with the following modes. Vendor provided MPI might already be installed. IBM, SGI, Cray etc provide their own:./config/confiure.py -with-cc=mpcc -with-fc=mpf77. If using MPICH which is already installed perhaps using myrinet/gm then use without specifying -with-cc=gcc etc.so that configure picks up mpicc from mpi-dir:./configure -with-mpi-dir=/path-to-mpich-install. You can build (sequential) PETSc without an MPI. This is useful for quickly installing PETSc if MPI is not available - for whatever reason.
Mpich Download
However - if there is any MPI code in user application, then its best to install a full MPI - even if the usage is currently limited to uniprocessor mode./configure -with-mpi=0 Installing with Open MPI with shared MPI libraries: OpenMPI defaults to building shared libraries for MPI. However, the binaries generated by MPI wrappers mpicc/mpif77 etc require LDLIBRARYPATH to be set to the location of these libraries. Due to this OpenMPI restriction one has to set LDLIBRARYPATH correctly per OpenMPI installation instructions, before running PETSc configure. If you do not set this environmental variables you will get messages when running./configure such as UNABLE to EXECUTE BINARIES for config/configure.py - Cannot run executables created with C. If this machine uses a batch system to submit jobs you will need to configure using/configure.py with the additional option -with-batch. Otherwise there is problem with the compilers.
Cygwin Install Make
Can you compile and run code with your C/C (and maybe Fortran) compilers? Or when running a code compiled with OpenMPI -bash-3.3$./conftest./conftest: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory Notes:. Avoid specifing compilers with options -with-cc or -with-fc when using the option -with-mpi-dir. Option -with-mpi-dir specifies using MPI compilers - so its best to use them - and not overwride them with user specified -with-cc. One can specify mpiexec or mpiexec with the options -with-mpiexec. If one wants to install PETSc with sources in a common system location like /usr/local or /opt, then we suggest creating a dir for PETSc in the required location with user privileges, and then do the PETSc install as a regular/non-root user.
sudo mkdir /opt/petsc. sudo chown user:group /opt/petsc.
Yum Install Mpich
cd /opt/petsc. tar -xzf petsc-3.8.0.tar.gz. cd petsc-3.8.0./configure. make Installing with -prefix: One can also use the GNU -prefix install mode./configure -prefix=/opt/petsc/petsc-3.8.0 other configure options. make. sudo make install.
user can now use this PETSc install with: make PETSCDIR=/opt/petsc/petsc-3.8.0 ex1 Note: one has to switch to using PETSCDIR=/opt/petsc/petsc-3.8.0 after install is done - and NOT use PETSCARCH anymore.