3 \page ghs3dprl_hypo_page GHS3DPRL Parameters hypothesis
5 \n GHS3DPRL Parameters hypothesis works only with <b>Tetrahedron (Tepal with TetMesh-GHS3D)</b> algorithm.
6 This algorithm is a commercial software, its use requires a licence (http://www.distene.com/fr/build/offer.html).
7 \n Tepal_V1.4 gives the possibility to generate a partitioned
8 mesh with 200 million tetrahedrons on a computer with average memory size
9 (2Go RAM) in about 50 hours on one CPU (Xeon, 2008).
10 \n New Tepal_V2.0 gives the possibility to generate a partitioned mesh with (for the moment) no more than 100 million
11 tetrahedrons on computers using MPI, (Total 16 Go RAM)
12 in about 900 seconds (!yes! : !seconds!) on 2 octo processors (Xeon, 2009).
13 The launch of this beta-version is described below.
14 \n This is a serious alternative to GHS3D, which requires a much less common
15 configuration with 64Go RAM to only try to make a partition of a mesh with
16 200 million tetrahedrons, no result guaranteed.
18 \note The Plugin doesn't load in the Memory the supposedly large resulting meshes.
19 The meshes are saved in MED files and can be imported in the user-defined location via menu File-Import-MED Files.
20 \n Pay attention, that Salome GUI needs 2Go RAM to load a MED
21 file with 5 million tetrahedrons.
23 \image html ghs3dprl_parameters_basic.png
27 <b>Name</b> - allows to define the name of the hypothesis (GHS3DPRL Parameters by default).
30 <b>MED_Name</b> - allows to define the path and the prefix of the
31 resulting MED files ("DOMAIN" by default).
32 If the path is not defined, the environment variable $SALOME_TMP_DIR
33 is used. If $SALOME_TMP_DIR is not defined as well, the environment
34 variable $TMP is used.
37 <b>Nb_Part</b> - allows to define the number of generated MED files.
38 The initial skin (triangles) will be meshed (tetrahedrons) and partitioned
39 in Nb_Part by the elementary algorithm implemented in Tepal.<br>
42 <b>Keep_Files</b> - if this box is checked, input files of Tepal
43 (GHS3DPRL.points and GHS3DPRL.faces) are not deleted after use (...if the
44 background mode was not used).
47 <b>Tepal_in_Background</b> - if this box is checked, Tepal execution
48 and MED file generation are launched in background mode and the user
49 can even exit Salome. Pay attention that in this case Tepal algorithm works
50 independently of "killSalome.py", and sometimes on another host.
53 <b>To_Mesh_Holes</b> - if this box is checked, the parameter component
54 of tetmesh-ghs3d will mesh holes.
57 <h1>Modifying GHS3DPRL Advanced Parameters</h1><br>
58 GHS3DPRL Plugin launches a standalone binary executable tepal2med.<br>
59 tepal2med launches tepal, waits for the end of computation, and
60 converts the resulting output tepal files into MED files.<br>
61 Some advanced optional parameters are accessible as arguments.<br>
63 If keep_files option is checked, it is possible to re-launch tepal2med
64 or tepal in the Terminal as a command with custom parameters.<br>
67 <b>Advanced tepal2med Parameters</b> - type "tepal2med --help" in the Terminal. <p>
70 myname@myhost > /export/home/myname/salome_5/GHS3DPRLPLUGIN_5/bin/salome/tepal2med --help
72 --help : produces this help message
73 --casename : path and name of input tepal2med files which are
74 - output files of tepal .msg .noboite .faces .points .glo
75 - output file of GHS3DPRL_Plugin casename_skin.med (optional)
76 with initial skin and its initial groups
77 --number : number of partitions
78 --medname : path and name of output MED files
79 --limitswap : max size of working cpu memory (Mo) (before swapping on .temp files)
80 --verbose : trace of execution (0->6)
81 --test : more tests about joints, before generation of output files
82 --menu : a GUI menu for option number
83 --launchtepal : also launch tepal on files casename.faces and casename.points and option number
84 --meshholes : force parameter component of tetmesh-ghs3d to mesh holes
85 --background : force background mode from launch tepal and generation of final MED files (big meshes)
86 --deletegroups : regular expression (see QRegExp) which matches unwanted groups in final MED files
87 (try --deletegroups="(\bAll_Nodes|\bAll_Faces)"
88 (try --deletegroups="((\bAll_|\bNew_)(N|F|T))"
90 tepal2med --casename=/tmp/GHS3DPRL --number=2 --medname=DOMAIN --limitswap=1000
91 --verbose=0 --test=yes --menu=no --launchtepal=no
97 <b>Advanced Tepal_V1.4 Parameters</b> <p>
101 USAGE : tepal options
104 --filename name (-f name) :
105 Prefix of the input case (MANDATORY)
108 Number of subdomains to make (MANDATORY)
110 --ghs3d ghs3d options (-g ghs3d options) :
111 Runs temesh ghs3d on a previously generated subdomain. (ghs3d options must be "quoted")
114 Max amount of memory (megabytes) allowed for ghs in the cutting process. (default is 0 : unlimited)
117 Only (re)meshes all subdomains and updates communications messages
119 --mesh_call command (-c command) :
120 Calls the user specified command for meshing all the
121 subomains after their skin has been generated
124 Only computes and shows some statistics on subdomains
127 Merges final subdomains skins
129 --rebuild_tetra (-R ) :
130 Merges final subdomains skins and tetraedra
132 --rebuild_iface (-i ) :
133 Includes interfaces in final subdomains merge
135 --rebuild_retag (-t ) :
136 Tags vertices, faces (and tetra if selected) with their
137 subdomain number in the final merge of subdomains (keeps the lowest tag for shared elements)
139 --rebuild_ensight_parts (-e ) :
140 Builds ensight geom file with parts
142 --tetmesh_args str (-G str) :
143 Arguments to pass to Tetmesh during cutting process
149 <b>Advanced ghs3d Parameters (through Tepal_V1.4's --tetmesh_args)</b> - type "ghs3d -h" in a Terminal. <p>
152 myname@myhost > ghs3d -h
155 /export/home/myname/ghs3d-4.0/DISTENE/Tools/TetMesh-GHS3D4.0/bin/Linux/ghs3dV4.0
156 [-u] [-m memory>] [-M MEMORY] [-f prefix] [-v verbose]
157 [-c component] [-p0] [-C] [-E count] [-t] [-o level]
158 [-I filetype] [-a/-b] [-O n m]
162 -u (-h) : prints this message.
164 -m memory : launches the software with memory in Megabytes.
165 The default value of this parameter is 64 Megabytes and its
166 minimum value is 10 Megabytes.
167 It is also possible to set this parameter with the
168 environment variable GHS3D_MEMORY by means of an operation
170 setenv GHS3D_MEMORY memory,
171 the value specified in the command line has the priority on
172 the environment variable.
174 -M MEMORY : provides the automatic memory adjustment feature.
175 If MEMORY (in Megabytes) is equal to zero, the size of the work space is
176 calculated from the input. If MEMORY is not equal to
177 zero, the software starts with MEMORY amount of work space.
178 The software reallocates memory as necessary.
179 The start value of MEMORY can range from 0 to 64 Megabytes,
180 the maximum depends on -m option and the actual memory available.
182 -f prefix : defines the generic prefix of the files.
184 -v verbose : sets the output level parameter (the verbose parameter
185 must be in the range 0 to 10).
187 -c component : chooses the meshed component. If the parameter is
188 0, all components will be meshed, if
189 1, only the main (outermost) component will be meshed
191 -p0 : disables creation of internal points.
193 -C : uses an alternative boundary recovery mechanism. It should be used only
194 when the standard boundary recovery fails.
196 -E count : sets the extended output for error messages. If -E is used,
197 the error messages will be printed, it is possible
198 to indicate the maximum number of printed messages between 1 and 100.
200 -t : generates an error file prefix.Log
202 -o level : sets the required optimisation level.
203 Valid optimisation levels are:
204 none, light, standard or strong,
205 with increase of "quality vs speed" ratio.
207 -I filetype : defines the input mesh format as follows:
208 -IP input files are ascii files, named prefix.points
209 and prefix.faces - this is the default type of files
210 -IPb input files are binary files, named prefix.pointsb
212 -IM input file is ascii file, named prefix.mesh
213 where prefix is defined with -f option
215 -a/-b : selects the output file type:
216 -a for ascii (the default) and
219 -On : saves a NOPO file in addition. NOPO is the mesh data
220 structure of the Simail and Modulef software packages.
221 -Om : saves a mesh file in addition.
222 -Omn : saves both NOPO and mesh files.
224 ==============================================================================
225 TETMESH-GHS3D SOFTWARE 4.0-3 (December, 2006)
227 COPYRIGHT (C)1989-2006 INRIA ALL RIGHTS RESERVED
228 ==============================================================================
230 Phone: +33(0)1-69-26-62-10 Fax: +33(0)1-69-26-90-33
231 EMail: support@distene.com )
236 <h1>Saving user's preferred GHS3DPRL Advanced Parameters</h1><br>
237 GHS3DPRL Plugin launches standalone binary executable tepal2med.<br>
238 You may rename file tepal2med as tepal2med.exe for example, and replace
239 tepal2med by a shell script at your convenience to overriding parameters.
240 <br>... or else $PATH modification... .<br>Idem for file tepal.<br><br>
242 <b>Advanced tepal2med Parameters</b> - overriding parameter deletegroups<p>
243 You may rename tepal2med as tepal2med.exe for example.
247 #script tepal2med overriding parameter deletegroups
248 #we have renamed binary executable tepal2med as tepal2med.exe
249 #echo tepal2med initial parameters are $1 $2 $3 $4 ... or $*
252 tepal2med.exe $* --deletegroups="(\bAll_Nodes|\bAll_Faces)"
258 <b>Advanced Tepal_V1.4 Parameters</b> - overriding parameter component of ghs3d (to mesh holes). <p>
259 You may rename tepal as tepal.exe for example.
263 #script tepal overriding parameter component of tetmesh-ghs3d
264 #we have renamed binary executable tepal as tepal.exe
266 #optionnaly we could set licence only for us
267 DISTENE_LICENSE_FILE="Use global envvar: DLIM8VAR"
268 DLIM8VAR="dlim8 1:1:29030@is142356/0016175ef08c::a1ba1...etc...e19"
269 SIMULOGD_LICENSE_FILE=29029@is142356
271 tepal.exe $* --tetmesh_args "-c 0"
277 <b>Advanced tepal Parameters</b> - overriding launching tepal on other host. <p>
278 You may rename tepal as tepal.exe for example.
282 #script tepal overriding launching tepal on other host (tepal run 64 bits only)
283 #we have renamed binary executable tepal as tepal.exe
284 #common file system (same path) otherwise scp... on input or result files
285 #ssh -keygen -t rsa done and files id_rsa et id-rsa.pub move in ~/.ssh
287 #example of typical command
288 #tepal -f /home/myname/tmp/GHS3DPRL -n 4 > /home/myname/tmp/tepal.log
289 #echo parameters $1 $2 $3 $4 ... or $*
291 #tepal licence ought to be known on otherhost
292 ssh otherhost "tepal.exe $* > /home/myname/tmp/tepal.log"
295 #ssh otherhost "tepal.exe $* --tetmesh_args \"-c 0\"" > /home/myname/tmp/tepal.log
301 <h1>Tepal_V2.0 and MPI use.</h1><br>
302 This all new beta-version needs MPI, (openmpi-1.3.1 was used). To use it you have to proceed
303 as done in "overriding parameter component of ghs3d".
304 Advanced ghs3d Parameters (through Tepal_V1.4's --tetmesh_args) are not assumed yet.
306 \n You may rename tepal as tepal64_v2.exe for example, and replace tepal by a shell script like below.
309 <b>example tepal_v2_mpirun.</b><p>
314 #script tepal overriding launching Tepal_V2.0 with MPI (tepal run 64 bits only).
315 #we have renamed binary executable tepal as tepal64_v2.exe.
316 #typical command to launch tepal v1 :
317 #tepal -f /tmp/myname/GHS3DPRL -n 16 > /tmp/myname/tepal.log
318 #this file is an exemple to transform this call for tepal v2.0,
319 # (beta version using .mesh input file)
320 #you have to adapt for your convenience.
322 #first problem is convert v1 input files GHS3DPRL.faces and GHS3DPRL.points
323 # to v2 input file GHS3DPRL.mesh.
324 #second problem is to launch on heterogeneous system linux cluster of
325 # 2 hosts (64 bits) of 8 nodes (by example)
326 # with different 2 executables codes linked on 2 different
327 # openmpi shared library codes.
328 #third problem is convert tepal v2 output files GHS3DPRL*.mesh
329 # to v1 input files GHS3DPRL*.faces an GHS3DPRL*.points.
331 #you have to work on the same physical disk and same path input and ouput files : $SAME_DIR
332 #you have to work on different physical disk but same path and name for executable files
333 # (and shared libraries) : $DIFF_DIR
335 echo "parameter 0="$0
336 echo "parameter 1="$1
337 echo "parameter 2="$2
338 echo "parameter 3="$3
339 echo "parameter 4="$4
341 export SAME_DIR=/same_physical_disk_and_same path/tmp
342 export DIFF_DIR=/different_physical_disk_but_same path/myname
344 #copy input local files from local current directory (something like /tmp/myname)
345 #in this case we need /tmp/myname and $SAME_DIR different
350 export IN_FILES=`basename $2`
351 export IN_DIR=`dirname $2`
352 #created .mesh from .faces et .points
353 /through_salome_path/facespoints2mesh.py $IN_FILES
355 #there are 2 executable openmpi and library through 2 physical DIFF_DIR
356 export PATH=$DIFF_DIR/openmpi-1.3.1_install/bin:${PATH}
357 export LD_LIBRARY_PATH=$DIFF_DIR/openmpi-1.3.1_install/lib:${LD_LIBRARY_PATH}
359 #there are 2 executables tepal_v2 through 2 physical DIFF_DIR
360 export LD_LIBRARY_PATH=$DIFF_DIR/tepal-2.0.0/bin/Linux_64:${LD_LIBRARY_PATH}
361 export PATH=$DIFF_DIR/tepal-2.0.0/bin/Linux_64:$PATH
363 #small test betweeen friends
365 #mpirun -n $4 hostname >> hostnames.log
367 #there necessary set env licence file for tepal v2
368 export DISTENE_LICENSE_FILE="Use global envvar: DLIM8VAR"
369 export DLIM8VAR="dlim8 1:1:29030@is142356/0016175ef08c::a1ba...9e19"
370 export SIMULOGD_LICENSE_FILE=29029@is142356
371 export LICENSE_FILE=/product/distene/dlim8.var.sh
373 #mpirun with necessary set envenvironment
374 export TMP_ENV="-x PATH -x LD_LIBRARY_PATH -x DISTENE_LICENSE_FILE -x DLIM8VAR \
375 -x SIMULOGD_LICENSE_FILE -x LICENSE_FILE"
376 #mpirun $TMPENV -n $4 which tepal64_v2.exe >> hostnames.log
378 #real mpirun uncomment after verify small test
379 mpirun $TMPENV -n $4 tepal64_v2.exe --in $IN_FILES.mesh --out $IN_FILES.mesh --verbose 100
381 #convert output files tepalv1 format
382 /through_salome_path/mesh2facespoints.py $IN_FILES
384 #copy ouputs files from $SAME_DIR to local current directory (something like /tmp/myname)
385 cp -f hostnames.log $IN_DIR
386 cp -f $IN_FILES* $IN_DIR
389 #cat $SAME_DIR/hostnames.log
390 #cat /tmp/myname/tepal.log
396 <h1>TUI use.</h1><br>
399 <b>example ex30_tepal.py.</b><p>
420 base = geompy.MakeVertex(0, 0, 0)
421 direction = geompy.MakeVectorDXDYDZ(0, 0, 1)
423 cylinder = geompy.MakeCylinder(base, direction, radius, height)
425 geompy.addToStudy(cylinder, "Cylinder")
427 # Define a mesh on a geometry
428 # ---------------------------
430 m = smesh.Mesh(cylinder)
432 # 2D mesh with BLSURF
433 # -------------------
435 algo2d = m.Triangle(smesh.BLSURF)
437 algo2d.SetPhysicalMesh(1)
440 algo2d.SetGeometricMesh(0)
445 algo3d = m.Tetrahedron(smesh.GHS3DPRL)
447 algo3d.SetMEDName(results)
449 algo3d.SetBackground(False)
450 algo3d.SetKeepFiles(False)
451 algo3d.SetToMeshHoles(True)
461 if os.access(results+".xml", os.F_OK):