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Setting runcase options
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=======================
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=======================
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The user may choose not to use the preprocessor
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(only for meshes in .tlc or .slc format) by setting
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otherwise set SOLCOM=0 as a standard
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WARNING: .slc and .tlc formats are obsolete and their use is deprecated.
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-------------------------------
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The variable COMMAND_REORIENT is used by the preprocessor to reorient cells and
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faces in case of incorrect orientation.
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COMMAND_REORIENT="--reorient"
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If no correction is necessary, the variable COMMAND_REORIENT is left emtpy, as:
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-------------------------------
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To join meshes with the preprocessor, additional options must be defined:
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- assign to the MESH variable the name of the meshes between " ".
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- assign to the COMMAND_JOIN variable the joining option. It is recommended
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to specify the color or group of the faces to be joined. If this can not
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be done, the options -color or -group should not be used (but the cost of
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the preprocessing will be higher and the process less robust). Selecting the
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faces can be performed by other means (see the preprocessor help by ecs -h).
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In the following example, the faces of color 3, 4 and 6 of the meshes
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titi.des and toto.unv are joined as:
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MESH="titi.des toto.unv"
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COMMAND_JOIN="-j --color 3 4 6"
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If no joining is necessary, the variable COMMAND_JOIN is left emtpy, as:
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-------------------------------
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when the Code_Saturne GUI is used, the user assigns the name of the
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xml file to the variable PARAM. The file should be placed in
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the directory DATA of the case.
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-------------------------------
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The variable COMMAND_CWF is used to cut the faces whose warp angle is larger
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than a given tolerance (in degrees). For instance, if the tolerance
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angle is 0.01 degrees (default value), the command reads:
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COMMAND_CWF="--cwf 0.01"
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If the user wants to use the mesh as obtained by the mesh generator,
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COMMAND_CWF is left empty, as:
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-------------------------------
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When periodicity applies, COMMAND_PERIO is used by the preprocessor,
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with the option --perio:
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Two types of periodicity are possible: translation and rotation.
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Translation : --perio --trans tx ty tz
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(tx,ty,tz): vector components
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Rotation : two methods are possible
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- the angle, the direction and an invariant point are given:
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--perio --rota --angle a --dir dx dy dz --invpt px py pz
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a : angle in degrees (between -180 and +180)
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(dx,dy,dz): rotation axis vector components
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(px,py,pz): rotation invariant point components
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- the matrix and an invariant point are given:
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--perio --rota --matrix m11 m12 m13 m21 m22 m23 m31 m32 m33 --invpt px py pz
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mij : matrix elements (line by line)
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(px,py,pz): rotation invariant point components
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Translation and rotation can be used together:
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--perio --trans tx ty tz --rota --angle a
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--dir dx dy dz -invpt px py pz
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or --perio --trans tx ty tz --rota --matrix m11 m12 m13
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The result is RoT (whatever the order of the rotation and translation in
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Rotation and translation have to be consistant with each other.
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It is better to use the faces where periodicity applies, by using the
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property of these faces, with their color for instance (faces
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can be selected by other means than their color: see ecs -h for more
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details), for instance:
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--perio --trans 10 0 0 --color 1 2
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Up to 3 periodicity directions can be imposed (one per spacial direction),
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--perio --trans 10 0 0 --perio --trans 0 1 0 --perio --trans 0 0 1
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If periodicity does not apply, COMMAND_PERIO is left empty as:
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Example ("\" shows the continuation of the command line):
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COMMAND_PERIO="--perio --trans -10.2 0 0 --color 2 \
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--perio --rota --angle 90 --dir 0 0 1 --invpt 0 0 0 \
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--perio --trans 0 1 0 \
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--rota --matrix 1 0 0 \
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0 1 0 --invpt 0 0 -0.2"
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-------------------------------
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If coupling with SYRTHES applies, (only one fluid simulation coupled
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with only one solid simulation), the necessary information is determined
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automatically by inspecting the user subroutines.
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For more complex (multiple) couplings, the script will have to be changed.
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-------------------------------
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If thermochemistry applies, the name of the thermochemistry data file
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may be specified through THERMOCHEMISTRY_DATA. For example:
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THERMOCHEMISTRY_DATA="dp_FCP"
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-------------------------------
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If meteo profiles are used, the name of the meteo data file
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may be specified through METEO_DATA. For example:
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-------------------------------
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User input files can be specified with the USER_INPUT_FILE variable
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(left empty if none are used) and the files are located in DATA.
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-------------------------------
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User output files to retrieve can be specified with USER_OUTPUT_FILE.
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-------------------------------
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The NUMBER_OF_PROCESSORS option defines the number of MPI processes to use
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(ideally equal to the physical number of processors or cores, but this
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is not mandatory). If the variable is left empty, it is determined
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automatically (for PC's or workstations, NUMBER_OF_PROCESSORS is set to 1
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and for clusters or supercomputers, it is set to the number of processors
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reserved for the batch job).
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When running a calculation through a batch system, it is not recommended
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to force NUMBER_OF_PROCESSORS to a value different from the number of
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processors required for the batch job, as oversubscribing may lead to
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strongly degraded performance (and may even fail depending on the system's
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mpi policy), and under-subscribing means reserving unused processors.
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When running the script interactively (such as on a Linux PC),
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NUMBER_OF_PROCESSORS may be set to a lower value than the number of
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physical processors (to limit system load), or to a higher value
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(usually for testing, as this reduces performance).
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When coupling with SYRTHES using MPI, one process/processor is reserved
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for SYRTHES, so the number of processors used for the kernel is
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equal to nproc_kernel = NUMBER_OF_PROCESSORS - 1.
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If we wish to specify distant machines (or are running on a cluster
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with no batch system), the optional PROCESSOR_LIST string may be defined.
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Running on multiple processors not reserved for this task is not recommended,
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as load imbalance due to 1 processor running multiple jobs is enough to
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degrade the performance for the whole job. Also, running in parallel without
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a high performance network will lead to low performance (low latency being
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even more important than high bandwidth).
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PROCESSOR_LIST="machine1 cpu=nb_cpu1 user=userid1 & machine2 cpu=nb_cpu2 user=userid2"
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PROCESSOR_LIST="machine1 & machine2"
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The & separates 2 machines in the list. Fields are as follows:
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machine1 and machine2 indicate machine names (as given by the
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for example: chi80xx.der.edf.fr
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nb_cpu1 and nb_cpu2 indicate the number of processors on hosts
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machine1 and machine2
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for example, on a dual-processor machine: cpu=2
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userid1 and userid2 indicate the user's login on machine1 and machine2
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Fields cpu= and user= are optional.
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The machine from which the script is run will automatically be used with
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most MPI environments.
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Selected machines must use a shared filesystem (at least NFS) and all
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be of the same general OS and architecture type.
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-------------------------------
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The CS_TMP_PREFIX variable allows the user to specify in which temporary
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directory the calculation will run. If left empty, a default directory
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will be used (architecture dependent). If a value is specified,
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the temporary directory will be:
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RUN=$CS_TMP_PREFIX/tmp_Saturne/$STUDY.$CASE.$DATE
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Specifying CS_TMP_PREFIX may be useful for example on a workstation so
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as to use a large local disk (CS_TMP_PREFIX=/local00/users/`whoami`
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Under some batch systems, the default of TMPDIR may be destroyed after
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each run, so to keep this temporary directory after the run,
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another value must be specified (CS_TMP_PREFIX=$SCRATCHDIR for example).
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-------------------------------
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The EXEC_PREPROCESS, EXEC_PARTITION, and EXEC_KERNEL variables allow running
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only some specific stages of the calculation, and saving them for future use.
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if EXEC_KERNEL is set to no, the Preprocessor's preprocessor_output file
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is copied in RESU, and the Partitioner's output is copied in a
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PARTITION_OUTPUT directory in RESU. note also that when partitioning with no
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kernel execution, the number of processors required is not known in advance,
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so the PARTITION_LIST variable must be used to indicate which partitionings
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are required. For example, PARTITION_LIST="128 256" will generate
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2 partitionings, with files domain_number_128 and domain_number_256
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in RESU/PARTITION_OUTPUT. The option "-no-perio" may also be added to
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PARTITION_LIST if we do not want periodicity to be accounted for in the
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If EXEC_PREPROCESS is set to no, a preprocessor_output file must be found in
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DATA (typically, a symbolic link to a file in RESU).
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If EXEC_PARTITION is set to no, a PARTITION_OUTPUT directory must be found
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in DATA (typically, a symbolic link to a file in RESU). If no partitioning
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is found, the calculation will continue, using an unoptimized partitioning,
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which may impact performance.
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-------------------------------
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Option CS_LIB_ADD is more advanced, mainly for developers.
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CS_LIB_ADD allows specifying external libraries to link. In this
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case, the whole option to pass to the linker must be given.
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CS_LIB_ADD="-L/home/saturne/opt/foo/lib -lfoo"
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VALGRIND enables running of the Kernel through Valgrind if this
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memory-checking tool is available (usually under Linux) To
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possibly with specific options, such as for example
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VALGRIND="valgrind --tool=memcheck"
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If valgrind is not in the PATH, its full path must be specified.
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ARG_CS_VERIF allows activation of elementary mesh quality tests,
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as well as basic linear algebra operations micro-benchmarks.
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="-q" : mesh quality criteria and test precision of gradient for
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sin(x+2y+3z) with each calculation mode (IMRGRA from 0 to 4)
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="--benchmark": basic linear algebra operation benchmark
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="--benchmark --mpitrace" : same as benchmark, with operations run
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only once, for use with MPI trace tools.
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In mesh quality or benchmark mode, no parameter file or user
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subroutine is needed.
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ARG_CS_OUTPUT allows redirection of output.
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The "--log" option allows redirecting output for a single-processor
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run or for rank 0 of a parallel run.
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"--log 0" output redirected to standard output
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"--log 1" output redirected to a "listing" file (default behavior)
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The "--logp" option allows redirection of output for ranks 1 to n-1
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for a parallel run on n processors:
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"--logp -1" turns off output for ranks > 0 (default behavior)
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"--logp 0" sends all output to the standard output (useful if every
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rank is associated to a different console, such as when running
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"--logp 1" redirects all output from ranks 1 to n-1 to files
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listing_n0002 to listing_n<N>.
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Options --log and --logp may be specified together or separately
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through the ARG_CS_OUTPUT variable.
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ECHO_SYR_COMM allows for echo of communications on the SYRTHES 3 side.
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This is only useful when debugging a coupled calculation.
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To activate this options, assign a strictly positive value to
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ECHO_SYR_COMM. For each message exchanged, the ECHO_SYR_COMM first
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and last values will be printed (characters, integers, or doubles).
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By default, the string is kept empty.
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Reasonable activation value:
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bin/runcase.help
