4.4. Installing SMITER GUI

To access SMITER source code repository it is technically necessary to have an ITER account and to have the necessary access control permissions. Both can be provided by sending a brief justifying email to mailto:Simon.Pinches@iter.org . Once the appropriate technical provisions have been made, it will be possible for the developer to log in to the web-based graphical frontend to the ITER IM software repositories to view the source code here: https://git.iter.org. Note that in addition to logging on to access the ITER intranet (if not on the IO LAN), it may also be necessary to authenticate to the Git front-end, particularly to browse restricted repositories. To download copies of repositories with restricted access and to gain write-access to any repository it is necessary to authenticate from the CLI. This is most conveniently done by uploading your public SSH key to the ITER Git server. The relevant link can be found under Manage Account in the top right-hand corner of the web front-end or accessed directly here: https://git.iter.org/plugins/servlet/ssh/account/keys. You will need to upload your public SSH key from each system you wish to access the ITER Git repositories from.

SMITER is an application with custom modules “based on” the SALOME “product”. Sources of custom modules are located under the module/ directory. The rest of the build is located under the BUILD/, SOURCES and INSTALL directory.

Quick build instructions from source code:

# https://git-scm.com/book/en/v2/Getting-Started-First-Time-Git-Setup
 git config --global color.ui auto
 git config --global --add alias.lol 'log --graph --decorate
    --abbrev-commit --all
    --pretty=format:"%C(auto)%h%d %C(blue)%an %C(red)%GG %C(reset)%s"'
 git clone ssh://git@git.iter.org/bnd/smiter.git
 git clone ssh://git@git.iter.org/bnd/smiter-aux.git
 cd smiter
 git checkout feature/salome
 cd salome
 make
 ./smiter

SMITER engine can be compiled with gfortran and the debug options intel_dbg and gfortran_dbg are also available. It may be helpful to note also that the commands:

./exec/decompile and ./exec/build

are provided for use after modifying source and/or when changing compilers. After the initial install, the compiler may be changed by going to the ./config directory and creating a new config.inc file (link), thus:

cd ./config;ln -sf config_new-compiler.inc config.inc

For compilation with MPI compiler can be changed from command line with:

env F90=mpif90 exec/build

Note

Note that if the Smiter checkout directory is anything else than ${HOME}/smiter then one needs to use SMITER_DIR environment variable for any building or cleaning command. For example:

cd ~/smiter-imas-8.5.2 env SMITER_DIR=${PWD} exec/decompile env SMITER_DIR=${PWD} exec/build

SMITER has a test-deck (data files for which are in the smiter-aux repo), see Test-Deck for more details, which should be used to check the installation. To build test-deck cases use:

cd ~/smiter-aux
git checkout feature/salome
./tests.bash

4.4.1. Building the SALOME framework and SMITER GUI application

The Makefile with:

make

builds everything from sources that are downloaded from external data or git repositories . Actually it resolves to the following set of commands that can also be entered manually:

make -C ARCHIVES
./sat prepare smiter # sources are unpacked and fetched
./sat clean smiter --build --install # if changing version
./sat --batch compile smiter # all sources are compiled and installed
./sat launcher smiter # script for launching smiter is prepared

Depending on hardware and/or software setup one can build SMITER GUI applications that differ in third-party prerequisites and module configurations/variants. It is advisable to try non-default smiter.pyconf in such cases. All SMITER applications are listed with:

./sat config --list

Please consult files in PROJECT/applications for details of individual applications. In cases when having problems with OpenGL one can try to build another application.

Building different SMITER GUI applications with make is possible by “exporting” environment variable SMITER_APPLICATION or providing it at every make command such as:

make SMITER_APPLICATION=smiter-8.5.2

However, it is more convenient to fix non-default application with

echo “SMITER_APPLICATION ?= smiter-8.5.2” > application.mk

and then this configuration will be used when variable is not set or provided at command line. When changing applications it is recommended to do:

make distclean all

To check which application will be used when building issue:

make query-SMITER_APPLICATION

In case of compile problems on a new machine, where some tools are missing to build SALOME prerequisites (libxmu-dev, bison, flex, …), one can observe failed ./sat log smiter

Some builds of prerequisites may be incomplete and can build OK but cause build failure in some dependent prerequisite later on due to missing system packages. Verify that 1. boost has 118+ files in lib/ installed 2. CAS has 224+ files in lib/ installed

If some prerequisite fails during compilation then it is advisable to do clean build. For example if metis fails with:

Compilation of metis ......................... KO

then one can observe failure with:

less LOGS/metis/script

and when problem resolved try to compile once again just metis with:

./sat prepare smiter-8.4.0 -p metis
./sat compile smiter-8.4.0 -p metis --clean_all

If OK is given at end of the compile then we can continue with make.

4.4.2. Developing and running SMITER

Global settings (editor, browser, log level) can be tuned with:

./sat config --edit

Prepare and compile SMITER with:

./sat prepare smiter --products SMITER,SMITER_PROFILE
./sat compile smiter --clean_all --products SMITER,SMITER_PROFILE
./sat launcher smiter

Error in SMITER module can be seen by the following command:

./sat log smiter

Click on the upper most command which failed and there you will see the debug messages of the build procedure.

To run the SMITER application use the ./sat run smiter

To recompile just SMITER module use:

./sat prepare smiter --products SMITER
./sat compile smiter --products SMITER --clean_install

4.4.3. Compiling with MPI

Smiter allows to run POWCAL in parallel with nearly linear scaling. To compile FORTRAN codes with MPI one needs to:

exec/decompile
env F90=mpif90 exec/build

and enable MPI run in SMITER GUI preferences. It is safe to run MPI compiled executables serialy without enabling MPI run.

4.4.4. Compiling documentation

HTML documentation is prepared during compilation of SMITER module automaticaly. For LaTeX documentation in PDF and writing its faster to compile documentation sources in build and launch environment. One can use:

make doc

or prepare environment with environment variables scripts for loading in command line that are created:

./sat environ smiter

Then one can:

source env_launch.sh

and prepare PDF or HTML documentation of the module:

cd SMITER/doc
make html
make latexpdf

that are then build as html/index.html and latex/solps-gui.pdf.

4.4.5. Catalog generator

SMITER component includes CORBA interface for calling by external programs, Python scripts and YACS schemas.

Required generation of the module/SMITER/resources/SMITERCatalog.xml.in can be achieved also by Tools –> Catalog generator Tool by selecting (Interface Data Language) IDL file and writing xml.in file with parameters as shown on the dialog.

../_images/catalog_generator.png

4.4.6. Building on ITER cluster

Different configurations are possible depending on IMAS git.iter.org access possibility and OpenGL graphics capabilities.

  1. smiter-imas-8.3.1 runs with software rendering with “old” SALOME version and ParaView 5.1 that uses OpenGL without GLSL
  2. smiter-imas-8.4.1 does not run with software rendering and work well with VirtualGL remotely.
  3. smiter-8.3.1 is without IMAS with Qt5.1 trah works software rendering.
  4. smiter-8.4.1 is without IMAS and no software rendering possible remotely as it is intended for VirtualGL remote rendering.
  5. smiter-8.4.0 works only on workstation with a graphics card due to newer Qt 5.9 libraries used.
  6. smiter-8.5.1 uses Qt 5.9.1 that works only on hardware graphics workstation.
  7. smiter-8.5.2 uses Qt 5.6.1 that works well with VirtualGL remote graphics.
  8. smiter-imas-8.5.x include IMAS support.

The best is to use the most recent 8.x version as they read HDF studies from previous versions and provide new features and improvements. Furthermore, we can have MPI or serial versions of SMARDDA kernel. This depends on the FOTRAN compiler selected. If F90 has mpi in its name.

For software rendering only SALOME 8.3.1 layer works unless 8.5.x is used with --use_mesa launcher. Temporary SOURCES and BUILD directories can be relinked to some faster local filesystem to speedup compilation as shown in the following build recipe that takes around 4 hours to build io-ls-titan.iter.org node.

export SAPP=smiter-imas-8.5.2 TMP=/dev/shm
git clone ssh://git@git.iter.org/bnd/smiter.git ${SAPP}
cd ${SAPP}
git checkout release/1.4
module purge # No modules needed besides system provided developer packages
cd salome
echo "SMITER_APPLICATION ?= ${SAPP}" > application.mk
rm -rf BUILD ${TMP}/${USER}/BUILD-${SAPP}     # We build on /tmp filesystem
mkdir -p ${TMP}/${USER}/BUILD-${SAPP}         # to speedup the compilation
ln -sf ${TMP}/${USER}/BUILD-${SAPP} BUILD     # and to resolve file locking
rm -rf SOURCES ${TMP}/${USER}/SOURCES-${SAPP} # issues with ParaView, lata,
mkdir -p ${TMP}/${USER}/SOURCES-${SAPP}       # and netgen. See ITSD-92745
ln -sf ${TMP}/${USER}/SOURCES-${SAPP} SOURCES # file locking report (open).
time make
# build SMARDDA now as Intel compiler available may interfere GUI build
cd ..
export SMITER_DIR=${PWD} F90=ifort
source Extras/setup
exec/build intel

SMITER and SALOME applications version 8.5.x can also be built with recent MESA software rendering library that is useful when no hardware graphics support is available. The MESA launcher can be built with

./sat launcher ${SAPP} --use_mesa

or simply with

make use_mesa

4.4.7. Building native SALOME GUI

If native SALOME GUI is also required to be build for providing GUI without SMITER then one needs to issue the following commands after SMITER was built

./sat prepare SALOME-8.5.2 -p SALOME
./sat compile SALOME-8.5.2 -p SALOME --clean_all
./sat launcher SALOME-8.5.2 # --use_mesa ## for 8.5.x software rendering
./salome

SMITER and SALOME GUI then coexists in the same installation directory. Therefore, SALOME versions must be the same. See smiter/salome/examples/modulefiles/iter/ for examples of TCL module files.

4.4.8. Build log

The following build logs shows build commands on ITER cluster login-01.iter.org login node.

[kosl@hpc-login01 ~]$ cd smiter/
[kosl@hpc-login01 smiter]$ exec/decompile
rm -f bsplvn.o bsplwn.o bvalue.o interu.o interv.o interw.o tb06a.o tc01a.o tg04a.o isnumb.o spleval.o msrect.o lowor.o isort.o cfftb1.o cffti1.o passb3.o passb5.o passf2.o passf4.o passf.o zfftf.o cfftf1.o passb2.o passb4.o passb.o passf3.o passf5.o zfftb.o zffti.o randlx.o
rm -f bsplvn.o bsplwn.o bvalue.o interu.o interv.o interw.o tb06a.o tc01a.o tg04a.o isnumb.o spleval.o msrect.o lowor.o isort.o cfftb1.o cffti1.o passb3.o passb5.o passf2.o passf4.o passf.o zfftf.o cfftf1.o passb2.o passb4.o passb.o passf3.o passf5.o zfftb.o zffti.o randlx.o
rm -f lib.a
rm -f bsplvn.o bsplwn.o bvalue.o interu.o interv.o interw.o tb06a.o tc01a.o tg04a.o isnumb.o spleval.o msrect.o lowor.o isort.o cfftb1.o cffti1.o passb3.o passb5.o passf2.o passf4.o passf.o zfftf.o cfftf1.o passb2.o passb4.o passb.o passf3.o passf5.o zfftb.o zffti.o randlx.o
rm -f libg.a
rm -f const_kind_m.o const_numphys_h.o date_time_m.o control_h.o dcontrol_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o beqan_h.o posang_h.o bcontrol_m.o vcontrol_h.o mcontrol_h.o mcontrol_m.o beq_m.o beqan_m.o posang_m.o bods_h.o geobjlist_h.o position_m.o fmesh_m.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o geobj_m.o stack_m.o query_m.o datline_h.o datline_m.o indict_m.o geobjlist_m.o geoq_m.o spl2d_m.o spl3d_m.o boutfile_m.o moutfile_m.o vfile_m.o gfile_m.o dfile_m.o geoq.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o date_time_m.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o pcontrol_h.o dcontrol_h.o pcontrol_m.o fmesh_m.o beq_m.o beqan_h.o beqan_m.o posang_m.o bods_h.o geobjlist_h.o position_m.o control_h.o vcontrol_h.o mcontrol_h.o mcontrol_m.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o geobj_m.o query_m.o datline_h.o datline_m.o geobjlist_m.o indict_m.o pcle_h.o pcle_m.o spl2d_m.o spl3d_m.o poutfile_m.o moutfile_m.o vfile_m.o gfile_m.o hdsfile_m.o nrsolve_m.o powelt_m.o powres_h.o powcal_h.o termplane_h.o edgprof_h.o edgprof_m.o termplane_m.o powcal_m.o odes_h.o odes_m.o stack_m.o powcal.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o scontrol_h.o scontrol_m.o date_time_m.o log_m.o clock_m.o position_m.o geobj_m.o posang_h.o bods_h.o geobjlist_h.o control_h.o li_m.o ld_m.o ls_m.o dbtree_h.o dbtree_m.o btree_m.o stack_m.o query_m.o spl2d_m.o spl3d_m.o geobjlist_m.o dcontrol_h.o vcontrol_h.o vfile_m.o gfile_m.o outfile_m.o position_h.o fmesh_h.o beq_h.o posang_m.o datline_h.o datline_m.o smanal_h.o smanal_m.o soutfile_m.o indict_m.o smanal.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o date_time_m.o mcontrol_h.o dcontrol_h.o apb_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o apb_m.o gfile_m.o spl3d_m.o spl2d_m.o position_m.o mcontrol_m.o moutfile_m.o magtfm.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o date_time_m.o control_h.o vcontrol_h.o dcontrol_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o spl2d_m.o spl3d_m.o geobjlist_h.o position_m.o ls_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o btree_m.o geobj_m.o query_m.o geobjlist_m.o indict_m.o vcontrol_m.o vfile_m.o gfile_m.o datline_h.o datline_m.o stack_m.o bods_h.o bods_m.o scontrol_h.o scontrol_m.o vtktfm.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o date_time_m.o control_h.o dcontrol_h.o log_m.o clock_m.o spl2d_m.o spl3d_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o geobjlist_h.o position_m.o li_m.o ld_m.o ls_m.o dbtree_h.o dbtree_m.o btree_m.o geobj_m.o query_m.o geobjlist_m.o indict_m.o dcontrol_m.o vcontrol_h.o vfile_m.o gfile_m.o datline_h.o datline_m.o dfile_m.o bods_h.o bods_m.o stlfile_m.o stack_m.o datvtk.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o control_h.o dcontrol_h.o vcontrol_h.o date_time_m.o control_m.o log_m.o clock_m.o position_m.o geobj_m.o posang_h.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o mtest_m.o termplane_h.o pcle_h.o pcle_m.o bods_h.o geobjlist_h.o geobjlist_m.o indict_m.o vfile_m.o outfile_m.o hdsfile_m.o query_m.o position_h.o fmesh_h.o beq_h.o posang_m.o datline_h.o datline_m.o stack_m.o spl2d_m.o spl3d_m.o hdsgen.o *.mod *.T
rm -f const_kind_m.o date_time_m.o log_m.o ccontrol_m.o ctlgen.o *.mod *.T
[kosl@hpc-login01 smiter]$ source Extras/setup
[kosl@hpc-login01 smiter]$ exec/decompile
rm -f bsplvn.o bsplwn.o bvalue.o interu.o interv.o interw.o tb06a.o tc01a.o tg04a.o isnumb.o spleval.o msrect.o lowor.o isort.o cfftb1.o cffti1.o passb3.o passb5.o passf2.o passf4.o passf.o zfftf.o cfftf1.o passb2.o passb4.o passb.o passf3.o passf5.o zfftb.o zffti.o randlx.o
rm -f bsplvn.o bsplwn.o bvalue.o interu.o interv.o interw.o tb06a.o tc01a.o tg04a.o isnumb.o spleval.o msrect.o lowor.o isort.o cfftb1.o cffti1.o passb3.o passb5.o passf2.o passf4.o passf.o zfftf.o cfftf1.o passb2.o passb4.o passb.o passf3.o passf5.o zfftb.o zffti.o randlx.o
rm -f lib.a
rm -f bsplvn.o bsplwn.o bvalue.o interu.o interv.o interw.o tb06a.o tc01a.o tg04a.o isnumb.o spleval.o msrect.o lowor.o isort.o cfftb1.o cffti1.o passb3.o passb5.o passf2.o passf4.o passf.o zfftf.o cfftf1.o passb2.o passb4.o passb.o passf3.o passf5.o zfftb.o zffti.o randlx.o
rm -f libg.a
rm -f const_kind_m.o const_numphys_h.o date_time_m.o control_h.o dcontrol_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o beqan_h.o posang_h.o bcontrol_m.o vcontrol_h.o mcontrol_h.o mcontrol_m.o beq_m.o beqan_m.o posang_m.o bods_h.o geobjlist_h.o position_m.o fmesh_m.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o geobj_m.o stack_m.o query_m.o datline_h.o datline_m.o indict_m.o geobjlist_m.o geoq_m.o spl2d_m.o spl3d_m.o boutfile_m.o moutfile_m.o vfile_m.o gfile_m.o dfile_m.o geoq.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o date_time_m.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o pcontrol_h.o dcontrol_h.o pcontrol_m.o fmesh_m.o beq_m.o beqan_h.o beqan_m.o posang_m.o bods_h.o geobjlist_h.o position_m.o control_h.o vcontrol_h.o mcontrol_h.o mcontrol_m.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o geobj_m.o query_m.o datline_h.o datline_m.o geobjlist_m.o indict_m.o pcle_h.o pcle_m.o spl2d_m.o spl3d_m.o poutfile_m.o moutfile_m.o vfile_m.o gfile_m.o hdsfile_m.o nrsolve_m.o powelt_m.o powres_h.o powcal_h.o termplane_h.o edgprof_h.o edgprof_m.o termplane_m.o powcal_m.o odes_h.o odes_m.o stack_m.o powcal.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o scontrol_h.o scontrol_m.o date_time_m.o log_m.o clock_m.o position_m.o geobj_m.o posang_h.o bods_h.o geobjlist_h.o control_h.o li_m.o ld_m.o ls_m.o dbtree_h.o dbtree_m.o btree_m.o stack_m.o query_m.o spl2d_m.o spl3d_m.o geobjlist_m.o dcontrol_h.o vcontrol_h.o vfile_m.o gfile_m.o outfile_m.o position_h.o fmesh_h.o beq_h.o posang_m.o datline_h.o datline_m.o smanal_h.o smanal_m.o soutfile_m.o indict_m.o smanal.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o date_time_m.o mcontrol_h.o dcontrol_h.o apb_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o apb_m.o gfile_m.o spl3d_m.o spl2d_m.o position_m.o mcontrol_m.o moutfile_m.o magtfm.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o date_time_m.o control_h.o vcontrol_h.o dcontrol_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o spl2d_m.o spl3d_m.o geobjlist_h.o position_m.o ls_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o btree_m.o geobj_m.o query_m.o geobjlist_m.o indict_m.o vcontrol_m.o vfile_m.o gfile_m.o datline_h.o datline_m.o stack_m.o bods_h.o bods_m.o scontrol_h.o scontrol_m.o vtktfm.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o date_time_m.o control_h.o dcontrol_h.o log_m.o clock_m.o spl2d_m.o spl3d_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o geobjlist_h.o position_m.o li_m.o ld_m.o ls_m.o dbtree_h.o dbtree_m.o btree_m.o geobj_m.o query_m.o geobjlist_m.o indict_m.o dcontrol_m.o vcontrol_h.o vfile_m.o gfile_m.o datline_h.o datline_m.o dfile_m.o bods_h.o bods_m.o stlfile_m.o stack_m.o datvtk.o *.mod *.T
rm -f const_kind_m.o const_numphys_h.o control_h.o dcontrol_h.o vcontrol_h.o date_time_m.o control_m.o log_m.o clock_m.o position_m.o geobj_m.o posang_h.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o mtest_m.o termplane_h.o pcle_h.o pcle_m.o bods_h.o geobjlist_h.o geobjlist_m.o indict_m.o vfile_m.o outfile_m.o hdsfile_m.o query_m.o position_h.o fmesh_h.o beq_h.o posang_m.o datline_h.o datline_m.o stack_m.o spl2d_m.o spl3d_m.o hdsgen.o *.mod *.T
rm -f const_kind_m.o date_time_m.o log_m.o ccontrol_m.o ctlgen.o *.mod *.T
[kosl@hpc-login01 smiter]$ exec/build intel
SMARDDA/SMITER modules must lie under directory $SMITER_DIR = /home/ITER/kosl/smiter
you may want to add 'source /home/ITER/kosl/smiter/Extras/setup' to your .bashrc file
ifort -r8 -save -O  -c -o bsplvn.o bsplvn.f
ifort -r8 -save -O  -c -o bsplwn.o bsplwn.f
ifort -r8 -save -O  -c -o bvalue.o bvalue.f
ifort -r8 -save -O  -c -o interu.o interu.f
ifort -r8 -save -O  -c -o interv.o interv.f
ifort -r8 -save -O  -c -o interw.o interw.f
ifort -r8 -save -O  -c -o tb06a.o tb06a.f
ifort -r8 -save -O  -c -o tc01a.o tc01a.f
ifort -r8 -save -O  -c -o tg04a.o tg04a.f
ifort -r8 -save -O  -c -o isnumb.o isnumb.f
ifort -r8 -save -O  -c -o spleval.o spleval.f
ifort -r8 -save -O  -c -o msrect.o msrect.f
ifort -r8 -save -O  -c -o lowor.o lowor.f
ifort -r8 -save -O  -c -o isort.o isort.f
ifort -r8 -save -O  -c -o cfftb1.o cfftb1.f
ifort -r8 -save -O  -c -o cffti1.o cffti1.f
ifort -r8 -save -O  -c -o passb3.o passb3.f
ifort -r8 -save -O  -c -o passb5.o passb5.f
ifort -r8 -save -O  -c -o passf2.o passf2.f
ifort -r8 -save -O  -c -o passf4.o passf4.f
ifort -r8 -save -O  -c -o passf.o passf.f
ifort -r8 -save -O  -c -o zfftf.o zfftf.f
ifort -r8 -save -O  -c -o cfftf1.o cfftf1.f
ifort -r8 -save -O  -c -o passb2.o passb2.f
ifort -r8 -save -O  -c -o passb4.o passb4.f
ifort -r8 -save -O  -c -o passb.o passb.f
ifort -r8 -save -O  -c -o passf3.o passf3.f
ifort -r8 -save -O  -c -o passf5.o passf5.f
ifort -r8 -save -O  -c -o zfftb.o zfftb.f
ifort -r8 -save -O  -c -o zffti.o zffti.f
ifort -save -O -c randlx.f
ar ru lib.a bsplvn.o bsplwn.o bvalue.o interu.o interv.o interw.o tb06a.o tc01a.o tg04a.o isnumb.o spleval.o msrect.o lowor.o isort.o cfftb1.o cffti1.o passb3.o passb5.o passf2.o passf4.o passf.o zfftf.o cfftf1.o passb2.o passb4.o passb.o passf3.o passf5.o zfftb.o zffti.o randlx.o
ar: creating lib.a
ranlib lib.a
mpif90 -O3  -DWITH_MPI -c const_kind_m.F90
mpif90 -O3  -DWITH_MPI -c const_numphys_h.F90
mpif90 -O3  -DWITH_MPI -c date_time_m.F90
mpif90 -O3  -DWITH_MPI -c position_h.F90
mpif90 -O3  -DWITH_MPI -c control_h.F90
mpif90 -O3  -DWITH_MPI -c dcontrol_h.F90
mpif90 -O3  -DWITH_MPI -c log_m.F90
mpif90 -O3  -DWITH_MPI -c clock_m.F90
mpif90 -O3  -DWITH_MPI -c fmesh_h.F90
mpif90 -O3  -DWITH_MPI -c position_m.F90
mpif90 -O3  -DWITH_MPI -c spl2d_m.F90
mpif90 -O3  -DWITH_MPI -c spl3d_m.F90
mpif90 -O3  -DWITH_MPI -c beq_h.F90
mpif90 -O3  -DWITH_MPI -c beqan_h.F90
mpif90 -O3  -DWITH_MPI -c posang_h.F90
mpif90 -O3  -DWITH_MPI -c fmesh_m.F90
mpif90 -O3  -DWITH_MPI -c posang_m.F90
mpif90 -O3  -DWITH_MPI -c beqan_m.F90
mpif90 -O3  -DWITH_MPI -c gfile_m.F90
mpif90 -O3  -DWITH_MPI -c beq_m.F90
mpif90 -O3  -DWITH_MPI -c bcontrol_m.F90
mpif90 -O3  -DWITH_MPI -c vcontrol_h.F90
mpif90 -O3  -DWITH_MPI -c mcontrol_h.F90
mpif90 -O3  -DWITH_MPI -c mcontrol_m.F90
mpif90 -O3  -DWITH_MPI -c bods_h.F90
mpif90 -O3  -DWITH_MPI -c geobj_m.F90
mpif90 -O3  -DWITH_MPI -c geobjlist_h.F90
mpif90 -O3  -DWITH_MPI -c ls_m.F90
mpif90 -O3  -DWITH_MPI -c query_m.F90
mpif90 -O3  -DWITH_MPI -c btree_m.F90
mpif90 -O3  -DWITH_MPI -c li_m.F90
mpif90 -O3  -DWITH_MPI -c ld_m.F90
mpif90 -O3  -DWITH_MPI -c dbtree_h.F90
mpif90 -O3  -DWITH_MPI -c dbtree_m.F90
mpif90 -O3  -DWITH_MPI -c stack_m.F90
mpif90 -O3  -DWITH_MPI -c datline_h.F90
mpif90 -O3  -DWITH_MPI -c datline_m.F90
mpif90 -O3  -DWITH_MPI -c indict_m.F90
mpif90 -O3  -DWITH_MPI -c geobjlist_m.F90
mpif90 -O3  -DWITH_MPI -c geoq_m.F90
mpif90 -O3  -DWITH_MPI -c boutfile_m.F90
mpif90 -O3  -DWITH_MPI -c moutfile_m.F90
mpif90 -O3  -DWITH_MPI -c vfile_m.F90
mpif90 -O3  -DWITH_MPI -c dfile_m.F90
mpif90 -O3  -DWITH_MPI -c geoq.F90
mpif90 -O3  -DWITH_MPI -o geoq const_kind_m.o const_numphys_h.o date_time_m.o control_h.o dcontrol_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o beqan_h.o posang_h.o bcontrol_m.o vcontrol_h.o mcontrol_h.o mcontrol_m.o beq_m.o beqan_m.o posang_m.o bods_h.o geobjlist_h.o position_m.o fmesh_m.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o geobj_m.o stack_m.o query_m.o datline_h.o datline_m.o indict_m.o geobjlist_m.o geoq_m.o spl2d_m.o spl3d_m.o boutfile_m.o moutfile_m.o vfile_m.o gfile_m.o dfile_m.o geoq.o  ./LIB/lib.a
mpif90 -O3  -DWITH_MPI -c termplane_h.F90
mpif90 -O3  -DWITH_MPI -c pcontrol_h.F90
mpif90 -O3  -DWITH_MPI -c odes_h.F90
mpif90 -O3  -DWITH_MPI -c powres_h.F90
mpif90 -O3  -DWITH_MPI -c edgprof_h.F90
mpif90 -O3  -DWITH_MPI -c edgprof_m.F90
mpif90 -O3  -DWITH_MPI -c powcal_h.F90
mpif90 -O3  -DWITH_MPI -c nrsolve_m.F90
mpif90 -O3  -DWITH_MPI -c odes_m.F90
odes_m.F90(1421): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.   [PDIA]
subroutine odes_rjfunct(pt,py,pydot,psi,pdia,pf,rjspl2d)
----------------------------------------^
mpif90 -O3  -DWITH_MPI -c pcle_h.F90
mpif90 -O3  -DWITH_MPI -c pcle_m.F90
mpif90 -O3  -DWITH_MPI -c powelt_m.F90
mpif90 -O3  -DWITH_MPI -c termplane_m.F90
mpif90 -O3  -DWITH_MPI -c powcal_m.F90
mpif90 -O3  -DWITH_MPI -c pcontrol_m.F90
mpif90 -O3  -DWITH_MPI -c poutfile_m.F90
mpif90 -O3  -DWITH_MPI -c hdsfile_m.F90
mpif90 -O3  -DWITH_MPI -c powcal.F90
mpif90 -O3  -DWITH_MPI -o powcal const_kind_m.o const_numphys_h.o date_time_m.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o pcontrol_h.o dcontrol_h.o pcontrol_m.o fmesh_m.o beq_m.o beqan_h.o beqan_m.o posang_m.o bods_h.o geobjlist_h.o position_m.o control_h.o vcontrol_h.o mcontrol_h.o mcontrol_m.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o geobj_m.o query_m.o datline_h.o datline_m.o geobjlist_m.o indict_m.o pcle_h.o pcle_m.o spl2d_m.o spl3d_m.o poutfile_m.o moutfile_m.o vfile_m.o gfile_m.o hdsfile_m.o nrsolve_m.o powelt_m.o powres_h.o powcal_h.o termplane_h.o edgprof_h.o edgprof_m.o termplane_m.o powcal_m.o odes_h.o odes_m.o stack_m.o powcal.o  ./LIB/lib.a
mpif90 -O3  -DWITH_MPI -c scontrol_h.F90
mpif90 -O3  -DWITH_MPI -c scontrol_m.F90
mpif90 -O3  -DWITH_MPI -c outfile_m.F90
mpif90 -O3  -DWITH_MPI -c smanal_h.F90
mpif90 -O3  -DWITH_MPI -c smanal_m.F90
mpif90 -O3  -DWITH_MPI -c soutfile_m.F90
mpif90 -O3  -DWITH_MPI -c smanal.F90
mpif90 -O3  -DWITH_MPI -o smanal const_kind_m.o const_numphys_h.o scontrol_h.o scontrol_m.o date_time_m.o log_m.o clock_m.o position_m.o geobj_m.o posang_h.o bods_h.o geobjlist_h.o control_h.o li_m.o ld_m.o ls_m.o dbtree_h.o dbtree_m.o btree_m.o stack_m.o query_m.o spl2d_m.o spl3d_m.o geobjlist_m.o dcontrol_h.o vcontrol_h.o vfile_m.o gfile_m.o outfile_m.o position_h.o fmesh_h.o beq_h.o posang_m.o datline_h.o datline_m.o smanal_h.o smanal_m.o soutfile_m.o indict_m.o smanal.o  ./LIB/lib.a
mpif90 -O3  -DWITH_MPI -c apb_h.F90
mpif90 -O3  -DWITH_MPI -c apb_m.F90
mpif90 -O3  -DWITH_MPI -c magtfm.F90
mpif90 -O3  -DWITH_MPI -o magtfm const_kind_m.o const_numphys_h.o date_time_m.o mcontrol_h.o dcontrol_h.o apb_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o apb_m.o gfile_m.o spl3d_m.o spl2d_m.o position_m.o mcontrol_m.o moutfile_m.o magtfm.o  ./LIB/lib.a
mpif90 -O3  -DWITH_MPI -c vcontrol_m.F90
mpif90 -O3  -DWITH_MPI -c bods_m.F90
mpif90 -O3  -DWITH_MPI -c vtktfm.F90
mpif90 -O3  -DWITH_MPI -o vtktfm const_kind_m.o const_numphys_h.o date_time_m.o control_h.o vcontrol_h.o dcontrol_h.o log_m.o clock_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o spl2d_m.o spl3d_m.o geobjlist_h.o position_m.o ls_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o btree_m.o geobj_m.o query_m.o geobjlist_m.o indict_m.o vcontrol_m.o vfile_m.o gfile_m.o datline_h.o datline_m.o stack_m.o bods_h.o bods_m.o scontrol_h.o scontrol_m.o vtktfm.o  ./LIB/lib.a
mpif90 -O3  -DWITH_MPI -c dcontrol_m.F90
mpif90 -O3  -DWITH_MPI -c stlfile_m.F90
mpif90 -O3  -DWITH_MPI -c datvtk.F90
mpif90 -O3  -DWITH_MPI -o datvtk const_kind_m.o const_numphys_h.o date_time_m.o control_h.o dcontrol_h.o log_m.o clock_m.o spl2d_m.o spl3d_m.o position_h.o fmesh_h.o beq_h.o posang_h.o posang_m.o geobjlist_h.o position_m.o li_m.o ld_m.o ls_m.o dbtree_h.o dbtree_m.o btree_m.o geobj_m.o query_m.o geobjlist_m.o indict_m.o dcontrol_m.o vcontrol_h.o vfile_m.o gfile_m.o datline_h.o datline_m.o dfile_m.o bods_h.o bods_m.o stlfile_m.o stack_m.o datvtk.o  ./LIB/lib.a
mpif90 -O3  -DWITH_MPI -c control_m.F90
mpif90 -O3  -DWITH_MPI -c mtest_m.F90
mpif90 -O3  -DWITH_MPI -c hdsgen.F90
mpif90 -O3  -DWITH_MPI -o hdsgen const_kind_m.o const_numphys_h.o control_h.o dcontrol_h.o vcontrol_h.o date_time_m.o control_m.o log_m.o clock_m.o position_m.o geobj_m.o posang_h.o ls_m.o btree_m.o li_m.o ld_m.o dbtree_h.o dbtree_m.o mtest_m.o termplane_h.o pcle_h.o pcle_m.o bods_h.o geobjlist_h.o geobjlist_m.o indict_m.o vfile_m.o outfile_m.o hdsfile_m.o query_m.o position_h.o fmesh_h.o beq_h.o posang_m.o datline_h.o datline_m.o stack_m.o spl2d_m.o spl3d_m.o hdsgen.o  ./LIB/lib.a
mpif90 -O3  -DWITH_MPI -c ccontrol_m.F90
mpif90 -O3  -DWITH_MPI -c ctlgen.F90
mpif90 -O3  -DWITH_MPI -o ctlgen const_kind_m.o date_time_m.o log_m.o ccontrol_m.o ctlgen.o  ./LIB/lib.a
mpif90 -O3  -DWITH_MPI -c parse.F90
mpif90 -O3  -DWITH_MPI -o parse parse.o
Warning - Documentation production requires doxygen at 1.8 or later
Warning: ignoring unsupported tag `SHOW_GROUPED_MEMB_INC  =' at line 522, file doxyfile
Warning: ignoring unsupported tag `DIA_PATH               =' at line 2081, file doxyfile
Warning: ignoring unsupported tag `DIAFILE_DIRS           =' at line 2287, file doxyfile
Parsing layout file DoxygenLayout.xml...
Searching for include files...
Searching for example files...
Searching for images...
Searching for files in directory /home/ITER/kosl/smiter/doc/images
Searching for dot files...
Searching for msc files...
Searching for files to exclude
Searching for files to process...
Searching for files in directory /home/ITER/kosl/smiter/doc
Reading and parsing tag files
Parsing files
Reading /home/ITER/kosl/smiter/doc/const_kind_m.f90...
Parsing file /home/ITER/kosl/smiter/doc/const_kind_m.f90...
Reading /home/ITER/kosl/smiter/doc/const_numphys_h.f90...
Parsing file /home/ITER/kosl/smiter/doc/const_numphys_h.f90...
Reading /home/ITER/kosl/smiter/doc/date_time_m.f90...
Parsing file /home/ITER/kosl/smiter/doc/date_time_m.f90...
Reading /home/ITER/kosl/smiter/doc/namelist.f90...
Parsing file /home/ITER/kosl/smiter/doc/namelist.f90...
Reading /home/ITER/kosl/smiter/doc/namelist_d.f90...
Parsing file /home/ITER/kosl/smiter/doc/namelist_d.f90...
Reading /home/ITER/kosl/smiter/doc/text.f90...
Parsing file /home/ITER/kosl/smiter/doc/text.f90...
Building group list...
Building directory list...
Building namespace list...
Building file list...
Building class list...
Associating documentation with classes...
Computing nesting relations for classes...
Building example list...
Searching for enumerations...
Searching for documented typedefs...
Searching for members imported via using declarations...
Searching for included using directives...
Searching for documented variables...
Building interface member list...
Building member list...
Searching for friends...
Searching for documented defines...
Computing class inheritance relations...
Computing class usage relations...
Flushing cached template relations that have become invalid...
Creating members for template instances...
Computing class relations...
Add enum values to enums...
Searching for member function documentation...
Building page list...
Search for main page...
Computing page relations...
Determining the scope of groups...
Sorting lists...
Freeing entry tree
Determining which enums are documented
Computing member relations...
Building full member lists recursively...
Adding members to member groups.
Computing member references...
Inheriting documentation...
Generating disk names...
Adding source references...
Adding xrefitems...
Sorting member lists...
Computing dependencies between directories...
Generating citations page...
Counting data structures...
Resolving user defined references...
Finding anchors and sections in the documentation...
Transferring function references...
Combining using relations...
Adding members to index pages...
Generating style sheet...
Generating search indices...
Generating example documentation...
Generating file sources...
Generating code for file const_kind_m.f90...
Generating code for file const_numphys_h.f90...
Generating code for file date_time_m.f90...
Generating code for file namelist.f90...
Generating code for file namelist_d.f90...
Generating code for file text.f90...
Generating file documentation...
Generating docs for file const_kind_m.f90...
Generating docs for file const_numphys_h.f90...
Generating docs for file date_time_m.f90...
Generating docs for file namelist.f90...
Generating docs for file namelist_d.f90...
Generating docs for file text.f90...
Generating page documentation...
Generating group documentation...
Generating class documentation...
Generating docs for compound const_kind_m...
Generating docs for compound const_numphys_h...
Generating docs for compound date_time_m...
Generating docs for nested compound date_time_m::date_time_t...
Generating docs for compound namelist...
Generating docs for nested compound namelist::analysisfiles...
Generating docs for nested compound namelist::beqparameters...
Generating docs for nested compound namelist::btreeparameters...
Generating docs for nested compound namelist::datvtkparameters...
Generating docs for nested compound namelist::edgprofparameters...
Generating docs for nested compound namelist::equilparameters...
Generating docs for nested compound namelist::hdsgenparameters...
Generating docs for nested compound namelist::inputfiles...
Generating docs for nested compound namelist::magfiles...
Generating docs for nested compound namelist::meshparameters...
Generating docs for nested compound namelist::miscparameters...
Generating docs for nested compound namelist::odesparameters...
Generating docs for nested compound namelist::panelarrayparameters...
Generating docs for nested compound namelist::plotselections...
Generating docs for nested compound namelist::positionparameters...
Generating docs for nested compound namelist::powcalparameters...
Generating docs for nested compound namelist::progfiles...
Generating docs for nested compound namelist::smanalparameters...
Generating docs for nested compound namelist::termplaneparameters...
Generating docs for nested compound namelist::vtkfiles...
Generating docs for nested compound namelist::vtktfmparameters...
Generating namespace index...
Generating graph info page...
Generating directory documentation...
Generating index page...
Generating file index...
Generating file member index...
Generating example index...
finalizing index lists...
lookup cache used 400/65536 hits=3872 misses=470
finished...
to access documentation type firefox  or xdg-open /home/ITER/kosl/smiter/doc/srcdoc/html/index.html

For building SMITER GUI it is advisable to have several CPUs available as it takes several hours to compile everything from scratch. See smiter/salome/README.md for up to date instructions.

Typical build log on CentOS 7 workstation with 20 cores is listed below

[kosl@io-ls-titan salome]$ time make
./sat prepare smiter-8.3.1
Clean the source directories ...OK
Getting sources of the application smiter-8.3.1
  workdir = /home/ITER/kosl/smiter/salome/salomeTools/..

Python:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/Python-2.7.10.tar.gz ... OK
Cython:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/Cython-0.23.2.tar.gz ... OK
numpy:                 arc:/home/ITER/kosl/smiter/salome/ARCHIVES/numpy-1.9.2.tar.gz ... OK
scipy:                 arc:/home/ITER/kosl/smiter/salome/ARCHIVES/scipy-0.15.1.tar.gz ... OK
lapack:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/lapack-3.5.0.tar.gz ... OK
cmake:                 arc:/home/ITER/kosl/smiter/salome/ARCHIVES/cmake-3.5.2.tar.gz ... OK
pyreadline:            arc:/home/ITER/kosl/smiter/salome/ARCHIVES/pyreadline-2.0.tar.gz ... OK
setuptools:            arc:/home/ITER/kosl/smiter/salome/ARCHIVES/setuptools-38.5.2.tar.gz ... OK
markupsafe:            arc:/home/ITER/kosl/smiter/salome/ARCHIVES/markupsafe-1.0.tar.gz ... OK
Jinja2:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/Jinja2-2.10.tar.gz ... OK
six:                   arc:/home/ITER/kosl/smiter/salome/ARCHIVES/six-1.11.0.tar.gz ... OK
distribute:            arc:/home/ITER/kosl/smiter/salome/ARCHIVES/distribute-0.6.28.tar.gz ... OK
pytz:                  arc:/home/ITER/kosl/smiter/salome/ARCHIVES/pytz-2018.3.tar.gz ... OK
pyparsing:             arc:/home/ITER/kosl/smiter/salome/ARCHIVES/pyparsing-2.2.0.tar.gz ... OK
dateutil:              arc:/home/ITER/kosl/smiter/salome/ARCHIVES/dateutil-2.4.0.tar.gz ... OK
freetype:              arc:/home/ITER/kosl/smiter/salome/ARCHIVES/freetype-2.4.11.tar.gz ... OK
matplotlib:            arc:/home/ITER/kosl/smiter/salome/ARCHIVES/matplotlib-1.4.3.tar.gz ... OK
cppunit:               arc:/home/ITER/kosl/smiter/salome/ARCHIVES/cppunit-1.13.2.tar.gz ... OK
qt:                    arc:/home/ITER/kosl/smiter/salome/ARCHIVES/qt-5.6.1-1.tar.gz ... OK
PyQt:                  arc:/home/ITER/kosl/smiter/salome/ARCHIVES/PyQt-5.6.tar.gz ... OK
qwt:                   arc:/home/ITER/kosl/smiter/salome/ARCHIVES/qwt-6.1.2.tar.bz2 ... OK
sip:                   arc:/home/ITER/kosl/smiter/salome/ARCHIVES/sip-4.18.tar.gz ... OK
omniORB:               arc:/home/ITER/kosl/smiter/salome/ARCHIVES/omniORB-4.1.6.tar.gz ... OK
omniORBpy:             arc:/home/ITER/kosl/smiter/salome/ARCHIVES/omniORBpy-3.6.tar.gz ... OK
boost:                 arc:/home/ITER/kosl/smiter/salome/ARCHIVES/boost-1.58.0.tar.gz ... OK
swig:                  arc:/home/ITER/kosl/smiter/salome/ARCHIVES/swig-2.0.8.tar.gz ... OK
gl2ps:                 arc:/home/ITER/kosl/smiter/salome/ARCHIVES/gl2ps-1.3.9p1.tar.gz ... OK
freeimage:             arc:/home/ITER/kosl/smiter/salome/ARCHIVES/freeimage-3.16.0.tar.gz ... OK
tcl:                   arc:/home/ITER/kosl/smiter/salome/ARCHIVES/tcl-8.6.0.tar.gz ... OK
tk:                    arc:/home/ITER/kosl/smiter/salome/ARCHIVES/tk-8.6.0.tar.gz ... OK
libxml2:               arc:/home/ITER/kosl/smiter/salome/ARCHIVES/libxml2-2.9.0.tar.gz ... OK
CAS:                   git:http://git.dev.opencascade.org/repos/occt.git tag:V7_1_0p1 ... OK
hdf5:                  arc:/home/ITER/kosl/smiter/salome/ARCHIVES/hdf5-1.8.14.tar.gz ... OK
ParaView:              arc:/home/ITER/kosl/smiter/salome/ARCHIVES/ParaView-5.1.2plus.tar.gz ... OK
metis:                 arc:/home/ITER/kosl/smiter/salome/ARCHIVES/metis-5.1.0.tar.gz ... OK
scotch:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/scotch-5.1.12b.tar.gz ... OK
med:                   arc:/home/ITER/kosl/smiter/salome/ARCHIVES/med-3.3.1.tar.gz ... OK
graphviz:              arc:/home/ITER/kosl/smiter/salome/ARCHIVES/graphviz-2.38.0p1.tar.gz ... OK
doxygen:               arc:/home/ITER/kosl/smiter/salome/ARCHIVES/doxygen-1.8.3.1.tar.gz ... OK
docutils:              arc:/home/ITER/kosl/smiter/salome/ARCHIVES/docutils-0.14.tar.gz ... OK
Sphinx:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/Sphinx-1.7.1p1.tar.gz ... OK
sphinx_rtd_theme:      arc:/home/ITER/kosl/smiter/salome/ARCHIVES/sphinx_rtd_theme-0.2.5b2.tar.gz ... OK
Pygments:              arc:/home/ITER/kosl/smiter/salome/ARCHIVES/Pygments-2.2.0.tar.gz ... OK
opencv:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/opencv-2.4.6.1.tar.gz ... OK
Homard:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/Homard-11.10.tar.gz ... OK
netgen:                arc:/home/ITER/kosl/smiter/salome/ARCHIVES/netgen-5.3.1.tar.gz ... OK
MeshGems:              arc:/home/ITER/kosl/smiter/salome/ARCHIVES/MeshGems-2.5-7p1.tar.gz ... OK
gmsh:                  arc:/home/ITER/kosl/smiter/salome/ARCHIVES/gmsh-3.0.5.tar.gz ... OK
cgns:                  arc:/home/ITER/kosl/smiter/salome/ARCHIVES/cgns-3.3.1.tar.gz ... OK
lata:                  arc:/home/ITER/kosl/smiter/salome/ARCHIVES/lata-1.3p3.tar.gz ... OK
CONFIGURATION:         git:http://git.salome-platform.org/gitpub/tools/configuration.git           tag:V8_3_0 ..... OK
SMITER_GUI:            DIR: /home/ITER/kosl/smiter/salome/salomeTools/../SMITER_GUI ... OK
SMITER:                DIR: /home/ITER/kosl/smiter/salome/salomeTools/../SMITER ... OK
MEDCOUPLING:           git:http://git.salome-platform.org/gitpub/tools/medcoupling.git             tag:V8_3_0 ..... OK
LIBBATCH:              git:http://git.salome-platform.org/gitpub/tools/libbatch.git                tag:V2_3_2 ..... OK
KERNEL:                git:http://git.salome-platform.org/gitpub/modules/kernel.git                tag:V8_3_0 ..... OK
GUI:                   git:http://git.salome-platform.org/gitpub/modules/gui.git                   tag:V8_3_0 ..... OK
GEOM:                  git:http://git.salome-platform.org/gitpub/modules/geom.git                  tag:V8_3_0 ..... OK
SMESH:                 git:http://git.salome-platform.org/gitpub/modules/smesh.git                 tag:V8_3_0 ..... OK
NETGENPLUGIN:          git:http://git.salome-platform.org/gitpub/plugins/netgenplugin.git          tag:V8_3_0 ..... OK
BLSURFPLUGIN:          git:http://git.salome-platform.org/gitpub/plugins/blsurfplugin.git          tag:V8_3_0 ..... OK
GHS3DPLUGIN:           git:http://git.salome-platform.org/gitpub/plugins/ghs3dplugin.git           tag:V8_3_0 ..... OK
GHS3DPRLPLUGIN:        git:http://git.salome-platform.org/gitpub/plugins/ghs3dprlplugin.git        tag:V8_3_0 ..... OK
HYBRIDPLUGIN:          git:http://git.salome-platform.org/gitpub/plugins/hybridplugin.git          tag:V8_3_0 ..... OK
HexoticPLUGIN:         git:http://git.salome-platform.org/gitpub/plugins/hexoticplugin.git         tag:V8_3_0 ..... OK
HEXABLOCK:             git:http://git.salome-platform.org/gitpub/modules/hexablock.git             tag:V8_3_0 ..... OK
HEXABLOCKPLUGIN:       git:http://git.salome-platform.org/gitpub/plugins/hexablockplugin.git       tag:V8_3_0 ..... OK
HOMARD:                git:http://git.salome-platform.org/gitpub/modules/homard.git                tag:V8_3_0 ..... OK
MED:                   git:http://git.salome-platform.org/gitpub/modules/med.git                   tag:V8_3_0 ..... OK
PARAVIS:               git:http://git.salome-platform.org/gitpub/modules/paravis.git               tag:V8_3_0 ..... OK
JOBMANAGER:            git:http://git.salome-platform.org/gitpub/modules/jobmanager.git            tag:V8_3_0 ..... OK
YACS:                  git:http://git.salome-platform.org/gitpub/modules/yacs.git                  tag:V8_3_0 ..... OK
YACSGEN:               git:http://git.salome-platform.org/gitpub/tools/yacsgen.git                 tag:V8_3_0 ..... OK
DOCUMENTATION:         git:http://git.salome-platform.org/gitpub/tools/documentation.git           tag:V8_3_0 ..... OK
SAMPLES:               git:http://git.salome-platform.org/gitpub/samples/datafiles.git             tag:V8_3_0 ..... OK
COMPONENT:             git:http://git.salome-platform.org/gitpub/samples/component.git             tag:V8_3_0 ..... OK

Getting sources of the application: OK (76 / 76)
Patching sources of the application smiter-8.3.1
  workdir = /home/ITER/kosl/smiter/salome/salomeTools/..

scipy:                   Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/scipy-0.14.1.patch
freetype:                Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/freetype-2.4.11_ft_export_FD20.patch
matplotlib:              Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/matplotlib_1_4_3_patch_freetype_detection_for_SAT.patch
  Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/matplotlib-1.4.3_no_auto_download.patch
  Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/matplotlib-1.4.3_fix_Cannot_connect_NavigationToolbar2QT.patch
  Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/matplotlib-1.4.3-enable-toolkits.patch
gl2ps:                   Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/gl2ps-1.3.9p1.patch
freeimage:               Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/freeimage-3.16.0_gcc6.patch
metis:                   Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/metis-use_cat_not_more.patch
  Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/metis-no-makeflags.patch
doxygen:                 Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/doxygen-1.8.3.1.patch
  Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/doxygen_compatibility_flex260.patch
opencv:                  Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/opencv-2.4.6.1-gcc6.patch
netgen:                  Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/netgen53ForSalome.patch
CONFIGURATION:           Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/Sphinx-configuration.patch
LIBBATCH:                Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/libbatch-src-Core-CommunicationProtocolSSH-X.patch
JOBMANAGER:              Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/JOBMANAGER-typos.patch
YACS:                    Apply patch /home/ITER/kosl/smiter/salome/PROJECT/products/patches/yacs_cea_v2.patch

Patching sources of the application: OK (76 / 76)
touch SOURCES/KERNEL SOURCES/GUI SOURCES/GEOM SOURCES/SMESH
make: Warning: File `SOURCES/GUI' has modification time 12 s in the future
./sat --batch compile smiter-8.3.1
Executing the compile commands in the build directories of the products of the application smiter-8.3.1
  SOURCE directory = /home/ITER/kosl/smiter/salome/SOURCES
   BUILD directory = /home/ITER/kosl/smiter/salome/BUILD

Compilation of Python ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of Python ........................                                                          Compilation of Python ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/Python
Compilation of libxml2 ....................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of libxml2 .......................                                                          Compilation of libxml2 ....................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/libxml2
Compilation of boost ......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of boost .........................                                                          Compilation of boost ......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/boost
Compilation of omniORB ....................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of omniORB .......................                                                          Compilation of omniORB ....................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/omniORB
Compilation of omniORBpy ..................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of omniORBpy .....................                                                          Compilation of omniORBpy ..................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/omniORBpy
Compilation of pyparsing ..................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of pyparsing .....................                                                          Compilation of pyparsing ..................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/pyparsing
Compilation of pytz .......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of pytz ..........................                                                          Compilation of pytz .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/pytz
Compilation of distribute .................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of distribute ....................                                                          Compilation of distribute .................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/distribute
Compilation of six ........................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of six ...........................                                                          Compilation of six ........................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/six
Compilation of setuptools .................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of setuptools ....................                                                          Compilation of setuptools .................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/setuptools
Compilation of Pygments ...................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of Pygments ......................                                                          Compilation of Pygments ...................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/Pygments
Compilation of docutils ...................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of docutils ......................                                                          Compilation of docutils ...................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/docutils
Compilation of dateutil ...................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of dateutil ......................                                                          Compilation of dateutil ...................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/dateutil
Compilation of markupsafe .................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of markupsafe ....................                                                          Compilation of markupsafe .................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/markupsafe
Compilation of Jinja2 ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of Jinja2 ........................                                                          Compilation of Jinja2 ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/Jinja2
Compilation of Sphinx ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of Sphinx ........................                                                          Compilation of Sphinx ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/Sphinx
Compilation of pyreadline .................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of pyreadline ....................                                                          Compilation of pyreadline .................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/pyreadline
Compilation of numpy ......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of numpy .........................                                                          Compilation of numpy ......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/numpy
Compilation of Cython ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of Cython ........................                                                          Compilation of Cython ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/Cython
Compilation of cmake ......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of cmake .........................                                                          Compilation of cmake ......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/cmake
Compilation of opencv ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of opencv ........................                                                          Compilation of opencv ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/opencv
Compilation of metis ......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of metis .........................                                                          Compilation of metis ......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/metis
Compilation of hdf5 .......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of hdf5 ..........................                                                          Compilation of hdf5 .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/hdf5
Compilation of cgns .......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of cgns ..........................                                                          Compilation of cgns .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/cgns
Compilation of med ........................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of med ...........................                                                          Compilation of med ........................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/med
Compilation of gl2ps ......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/gl2ps
Compilation of lapack ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of lapack ........................                                                          Compilation of lapack ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/lapack
Compilation of scipy ......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of scipy .........................                                                          Compilation of scipy ......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/scipy
Compilation of freetype ...................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of freetype ......................                                                          Compilation of freetype ...................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/freetype
Compilation of cppunit ....................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of cppunit .......................                                                          Compilation of cppunit ....................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/cppunit
Compilation of YACSGEN ....................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of YACSGEN .......................                                                          Compilation of YACSGEN ....................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/YACSGEN
Compilation of qt ............................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of qt ............................                                                          Compilation of qt ............................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/qt
Compilation of sip ........................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of sip ...........................                                                          Compilation of sip ........................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/sip
Compilation of qwt ........................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of qwt ...........................                                                          Compilation of qwt ........................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/qwt
Compilation of PyQt .......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of PyQt ..........................                                                          Compilation of PyQt .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/PyQt
Compilation of matplotlib .................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of matplotlib ....................                                                          Compilation of matplotlib .................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/matplotlib
Compilation of ParaView ...................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of ParaView ......................                                                          Compilation of ParaView ...................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/ParaView
Compilation of lata .......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of lata ..........................                                                          Compilation of lata .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/lata
Compilation of swig .......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of swig ..........................                                                          Compilation of swig .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/swig
Compilation of LIBBATCH ...................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/LIBBATCH
Compilation of freeimage ..................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of freeimage .....................                                                          Compilation of freeimage ..................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/freeimage
Compilation of tcl ........................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of tcl ...........................                                                          Compilation of tcl ........................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/tcl
Compilation of tk ............................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of tk ............................                                                          Compilation of tk ............................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/tk
Compilation of scotch ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of scotch ........................                                                          Compilation of scotch ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/scotch
Compilation of graphviz ...................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of graphviz ......................                                                          Compilation of graphviz ...................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/graphviz
Compilation of doxygen ....................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of doxygen .......................                                                          Compilation of doxygen ....................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/doxygen
Compilation of KERNEL ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/KERNEL
Compilation of DOCUMENTATION ................. OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/DOCUMENTATION
Compilation of CAS ........................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/CAS
Compilation of GUI ........................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/GUI
Compilation of YACS .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/YACS
Compilation of JOBMANAGER .................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/JOBMANAGER
Compilation of GEOM .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/GEOM
Compilation of HEXABLOCK ..................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/HEXABLOCK
Compilation of gmsh .......................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of gmsh ..........................                                                          Compilation of gmsh .......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/gmsh
Compilation of netgen ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of netgen ........................                                                          Compilation of netgen ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/netgen
Compilation of sphinx_rtd_theme .............. SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of sphinx_rtd_theme ..............                                                          Compilation of sphinx_rtd_theme .............. OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/sphinx_rtd_theme
Compilation of Homard ........................ SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of Homard ........................                                                          Compilation of Homard ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/Homard
Compilation of MeshGems ...................... SCRIPT /home/ITER/kosl/smiter/salome/PROJECT/products/comCompilation of MeshGems ......................                                                          Compilation of MeshGems ...................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/MeshGems
Compilation of CONFIGURATION ................. ignored
Compilation of MEDCOUPLING ................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/MEDCOUPLING
Compilation of COMPONENT ..................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/COMPONENT
Compilation of MED ........................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/MED
Compilation of SMESH ......................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/SMESH
Compilation of PARAVIS ....................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/PARAVIS
Compilation of HOMARD ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/HOMARD
Compilation of HEXABLOCKPLUGIN ............... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/HEXABLOCKPLUGIN
Compilation of HexoticPLUGIN ................. OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/HexoticPLUGIN
Compilation of HYBRIDPLUGIN .................. OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/HYBRIDPLUGIN
Compilation of GHS3DPRLPLUGIN ................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/GHS3DPRLPLUGIN
Compilation of GHS3DPLUGIN ................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/GHS3DPLUGIN
Compilation of BLSURFPLUGIN .................. OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/BLSURFPLUGIN
Compilation of NETGENPLUGIN .................. OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/NETGENPLUGIN
Compilation of SMITER ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/SMITER
Compilation of SMITER_GUI .................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/SMITER_GUI
Compilation of SAMPLES ....................... ignored

Compilation: OK (76/76)
touch INSTALL/KERNEL INSTALL/GUI INSTALL/GEOM INSTALL/SMESH
./sat prepare smiter-8.3.1 --product SMITER
Clean the source directories ...OK
Getting sources of the application smiter-8.3.1
  workdir = /home/ITER/kosl/smiter/salome/salomeTools/..

SMITER:               DIR: /home/ITER/kosl/smiter/salome/salomeTools/../SMITER ... OK

Getting sources of the application: OK (1 / 1)
Patching sources of the application smiter-8.3.1
  workdir = /home/ITER/kosl/smiter/salome/salomeTools/..


Patching sources of the application: OK (1 / 1)
./sat compile smiter-8.3.1 --product SMITER --clean_all
Executing the compile commands in the build directories of the products of the application smiter-8.3.1
  SOURCE directory = /home/ITER/kosl/smiter/salome/SOURCES
   BUILD directory = /home/ITER/kosl/smiter/salome/BUILD

Compilation of SMITER ........................ OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/SMITER

Compilation: OK (1/1)
./sat prepare smiter-8.3.1 --product SMITER_GUI
Clean the source directories ...OK
Getting sources of the application smiter-8.3.1
  workdir = /home/ITER/kosl/smiter/salome/salomeTools/..

SMITER_GUI:           DIR: /home/ITER/kosl/smiter/salome/salomeTools/../SMITER_GUI ... OK

Getting sources of the application: OK (1 / 1)
Patching sources of the application smiter-8.3.1
  workdir = /home/ITER/kosl/smiter/salome/salomeTools/..


Patching sources of the application: OK (1 / 1)
./sat compile smiter-8.3.1 --product SMITER_GUI --clean_all
Executing the compile commands in the build directories of the products of the application smiter-8.3.1
  SOURCE directory = /home/ITER/kosl/smiter/salome/SOURCES
   BUILD directory = /home/ITER/kosl/smiter/salome/BUILD

Compilation of SMITER_GUI .................... OK
INSTALL directory = /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/SMITER_GUI

Compilation: OK (1/1)
./sat launcher smiter-8.3.1
Generating launcher for smiter-8.3.1 :
  /home/ITER/kosl/smiter/salome/salomeTools/../INSTALL/SMITER_GUI/salome

real    319m21.533s
user    414m9.641s
sys     79m48.025s

4.4.9. Installation instructions for cluster admins

The follwing example works on ITER cluster running CentOS 7 and takes less than 4 hours to complete:

ssh io-ls-titan.iter.org
TAG=1.4.0
mkdir -p /work/imas/opt/SMITER
cd /work/imas/opt/SMITER/
git clone ssh://git@git.iter.org/bnd/smiter.git $TAG
cd $TAG
git checkout release/1.4
time ci_scripts/build_titan
mkdir -p /work/imas/etc/modulefiles/SMITER
cp salome/examples/modulefiles/iter/SMITER/* \
   /work/imas/etc/modulefiles/SMITER/
mkdir -p /work/imas/etc/modulefiles/SALOME
cp salome/examples/modulefiles/iter/SALOME/* \
  /work/imas/etc/modulefiles/SALOME/

Examine ci_scipts/ directory for similar continous integration scipts or use instructions below to build.

ci_scripts/install_smiter script that builds everything, installs and prepares modules for SALOME and SMITER. Installation is in separate directories and new versions of SMITER will reuse SALOME installation. The same goes if IMAS changes. Only new IMAS is installed and reused if no change in IMAS version. Just do:

cd ~/smiter/ && git pull
TARGET_ROOT=/tmp/$USER MODULEFILE_DIR=/tmp/$USER/modules \
ci_scripts/install_smiter

if you want to test the installation with

module use /tmp/$USER/modules

Then you can repeat installation with just

ci_scripts/install_smiter

that installs into default /work/imas/opt with modules in /work/imas/etc/modulefiles directory. Other variables are also settavbe therein.

4.4.10. Environment variables affecting SMITER GUI

SMITER does not require environment variables to be set as all are included in auto-generated launchers scripts. However, administrators may preset some settings to users using module environments in order to correctly use system dependent builds for MPI processing and example studies. These environment variables are:

SMITER_DIR

Point to the top directory where SMITER is installed or built. It is expected that subdirectory exec/ contains all compiled codes to be run by the GUI and that there is doc/ subdirectory with compiled reference manual that can be oppened at correct section when pressing Help button. If SMITER_DIR is not set the it is expected that ${HOME}/smiter/exec and ${HOME}/smiter/doc contain compiled files.

SMITER_MPI_DEFAULT_COMMAND

If set than this setting enforces and overrides default mpirun -np 4 command when using MPI on local workstation only. When utilizing cluster batch submission commands then this submission needs to be interactive and not detached. For example on ITER cluster the SLURM submission and OpenMPI that was compiled with MPI2 library provided by slurm-utils package can be set as:

env --unset=LD_PRELOAD srun -n 4 --mpi=pmi2 --tasks-per-node=2
    --constraint=ib_qdr --kill-on-bad-exit

to run on 4 processors specified to srun that does not finish until the code submitted exits. Note that there is no mpirun command needed when compiled with MPI2 library that determines run layout from the scheduler. Clearing LD_PRELOAD environment variable removes annoying VirtualGL “imposter” wrapping libraries message. Constraint to run on Infiniband (ib_qdr) can be removed when running on single node or having no such resource. Since communication between powcal processes is small SMITER runs well on clusters without Infiniband.

When using PBS/Torque/Maui schedulers then interactive commands can be obtained with:

env --unset=LD_PRELOAD qsub -I -V -N smiter -l nodes=2:ppn=12
 -x '/usr/mpich/bin/mpiexec -np 24 -machinefile %PBS_NODEFILE
     -wdir %PBS_O_WORKDIR %SMITER'

QSUB switches -I -x are providing interactive batch command needed for the workflow of codes.

The following variables are replaced at at submission:

%SMITER
Absolute path to SMITER code with arguments is replacing this variable.
%JOBNAME
Can be used instead of smiter following -N switch in above example.

Characters % are replaced with $ for ease of escaping in scripts, settings and module files. For example %PBS_NODEFILE is submitted as $PBS_NODEFILE at the command execution.

SMITER_MPI_SHELL_TYPE

Index of the shell used when submitted. For cases when the submission command does not provide TTY (standard output and input) streams one of the shells are required for that. Usually the need for shell is required when print output from codes in SMITER output window is desired. The following shell indexes can be set:

0
Execute <MPI run command> without a shell. This is the default if not specified but can be enforced.
1
bash -c "<MPI run command>" is used.
2
tcsh -c "<MPI run command>" is used.
3
ksh -c "<MPI run command>" is used.
SMITER_STUDY_EXAMPLES_DIR

If set then after SMITER module is activated the shortcut to study examples directory appears in File‣Open menu.