seissol / pumgen Goto Github PK

7.0 7.0 3.0 395 KB

Mesh generation for SeisSol

License: BSD 3-Clause "New" or "Revised" License

C++ 91.86% CMake 8.14%

pumgen's Introduction

SeisSol is a scientific software for the numerical simulation of seismic wave phenomena and earthquake dynamics. It is based on the discontinuous Galerkin method combined with ADER time discretization. Visit our official website and also read our documentation in order to learn more about SeisSol. Our discussion forum can help you to communicate with SeisSol developers or other users, share your ideas, ask questions, etc.

Note

SeisSol is still under heavy development and comes without any guaranteed funcitonality. At the moment we can only provide very limited support for general users.

Collaboration

If you are interested in a close collaboration, please, contact Alice Gabriel.

Code of Conduct

We follow a Code of Conduct. Please follow the rules when participating in our community.

Contributing

We will be happy if you plan to contribute new features, extensions or bug fixes to SeisSol. To start off, please, open a new issue and discuss your feature with us before diving into coding. Visit our doxygen documentation to learn more about the source code structure.

To learn more about contributing to SeisSol, please read our Contribution page.

pumgen's People

Contributors

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Forkers

sabrinakrallmann palgunadi1993 irsn

pumgen's Issues

Compilation error with GMSH support

Describe the issue:
Compiling pumgen (current master:498ab01) with
set(CMAKE_CXX_STANDARD 17) in CMakeLists.txt give CMake error:

Target "cmTC_9516a" requires the language dialect "CXX17" , but CMake does not know the compile flags to use to enable it.

then I tried changing CMakeLists.txt to set(CMAKE_CXX_STANDARD 11) removed previous CMake error and lead to another error:

PUMGen/src/third_party/GMSHLexer.h(49): error: "auto" function requires a trailing return type
auto getIdentifier() const { return identifier; }
PUMGen/src/third_party/GMSHLexer.h(50): error: "auto" function requires a trailing return type
auto getInteger() const { return integer; }
PUMGen/src/third_party/GMSHLexer.h(51): error: "auto" function requires a trailing return type
auto getReal() const { return real; }
PUMGen/src/third_party/GMSHLexer.h(52): error: "auto" function requires a trailing return type
auto getSourceLoc() const { return loc; }
PUMGen/src/third_party/GMSHParser.h(8): catastrophic error: cannot open source file "optional"
#include

I tried to exclude all related to GMSH from
a) on CMakeLists.txt:

${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/ParallelGMSHReader.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSHLexer.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSHParser.cpp

b) on src/pumgen.cpp:

#include "meshreader/ParallelGMSHReader.h"

remove "msh2":

const char* source[] = {"gambit", "fidap", "msh2", "netcdf", "apf", "simmodsuite"};

and remove "case 2" and modify other case numbers according number in case list:

    case 2:
       logInfo(rank) << "Using GMSH mesh format 2 (msh2) mesh";
       meshInput = new SerialMeshFile<puml::ParallelGMSHReader>(inputFile);
       break;

with this, pumgen compiled successfully.

To Reproduce:
intel/2017
mpi.intel/2017
cmake/3.10.3

cmake .. -DCMAKE_PREFIX_PATH=$pumiDir -DSIMMETRIX=ON
-DSIMMETRIX_ROOT=$simmetrixDir -DCMAKE_BUILD_TYPE=Release
-DCMAKE_C_COMPILER=mpiicc \
-DCMAKE_CXX_COMPILER=mpiicpc
make -j 4

Error while installing xml pumgen

Hi,

I got this error while compiling xml pumgen:

In file included from src/pumgen.cpp:38:
src/input/SimModSuite.h:557:12: error: no matching function for call to 'MS_setMeshSizePropagation'
MS_setMeshSizePropagation(meshCase,face,2,1,MeshAtt.MeshSizePropagationDistance,MeshAtt.MeshSizePropagationScalingFactor);
^~~~~~~~~~~~~~~~~~~~~~~~~
/project/k1343/palgunkh/myLibs/meshing_software/simmetrix/14.0-200424/include/MeshSim.h:149:21: note: candidate function not viable: requires 5 arguments, but 6 were provided
Meshing_EXPORT void MS_setMeshSizePropagation(pACase cs, pGEntity gent, int closure, double distance, double sizeFactor);
^
In file included from src/pumgen.cpp:38:
src/input/SimModSuite.h:566:92: warning: expression result unused [-Wunused-value]
logInfo(PMU_rank()) << "UseDiscreteMesh; faceid, noModification:"<<*it, MeshAtt.UseDiscreteMesh_noModification;
~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:631:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(ent = (pGEntity)PList_next(lsmallFeats,&iter)){
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:631:15: note: place parentheses around the assignment to silence this warning
while(ent = (pGEntity)PList_next(lsmallFeats,&iter)){
^
( )
src/input/SimModSuite.h:631:15: note: use '==' to turn this assignment into an equality comparison
while(ent = (pGEntity)PList_next(lsmallFeats,&iter)){
^
==
src/input/SimModSuite.h:642:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(vert = (pGVertex)PList_next(vertices,&iter2)){
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:642:20: note: place parentheses around the assignment to silence this warning
while(vert = (pGVertex)PList_next(vertices,&iter2)){
^
( )
src/input/SimModSuite.h:642:20: note: use '==' to turn this assignment into an equality comparison
while(vert = (pGVertex)PList_next(vertices,&iter2)){
^
==
src/input/SimModSuite.h:705:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (reg = RIter_next(reg_it)) {
~~~~^~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:705:20: note: place parentheses around the assignment to silence this warning
while (reg = RIter_next(reg_it)) {
^
( )
src/input/SimModSuite.h:705:20: note: use '==' to turn this assignment into an equality comparison
while (reg = RIter_next(reg_it)) {
^
==
src/input/SimModSuite.h:772:22: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(modelRegion=GRIter_next(modelRegions)) { // get the next model region
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:772:22: note: place parentheses around the assignment to silence this warning
while(modelRegion=GRIter_next(modelRegions)) { // get the next model region
^
( )
src/input/SimModSuite.h:772:22: note: use '==' to turn this assignment into an equality comparison
while(modelRegion=GRIter_next(modelRegions)) { // get the next model region
^
==
src/input/SimModSuite.h:787:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(modelFace=GFIter_next(modelFaces)) { // get the next model face
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
src/input/SimModSuite.h:787:20: note: place parentheses around the assignment to silence this warning
while(modelFace=GFIter_next(modelFaces)) { // get the next model face
^
( )
src/input/SimModSuite.h:787:20: note: use '==' to turn this assignment into an equality comparison
while(modelFace=GFIter_next(modelFaces)) { // get the next model face
^
==
src/input/SimModSuite.h:819:21: warning: unused variable 'hasnorm' [-Wunused-variable]
int hasnorm = SimPolygons_pointData(poly, polypoint[k], pntlocation, pntnormal);
^
src/input/SimModSuite.h:761:12: warning: unused variable 'edgeList' [-Wunused-variable]
pPList edgeList; // Edges bounding a face
^
src/input/SimModSuite.h:762:12: warning: unused variable 'thisEdge' [-Wunused-variable]
pGEdge thisEdge;
^
9 warnings and 1 error generated.
scons: *** [build/src/pumgen.o] Error 1
scons: building terminated because of errors.

Do I miss something?
Thank you.

Cheers,
Kadek

pumgen was not compiling because of hdf5

We tried installing pumgen on a new local cluster, and we had trouble linking hdf5 library.
This line was giving us trouble:
mpicc -o build/pumgen -fopenmp -Wl,-rpath=/lrz/sys/libraries/netcdf/4.3.3/intel/ibmmpi_poe1.4_1505/lib (...) lSimPartitionWrapper-mpich2 -lSimModel -lpskernel
something like undefined reference to H5_Close

And actually we solved it adding -lhdf5 to this line. So maybe something has to be updated in the install script.

Compiling with MPI 4

Compiling with the command on my local machine (Ubuntu 20.04)

cmake .. \
>   -DCMAKE_C_COMPILER="`which mpicc`" \
>   -DCMAKE_CXX_COMPILER="`which mpiCC`" \
>   -DCMAKE_C_FLAGS="-O2 -g -Wall" \
>   -DCMAKE_CXX_FLAGS="-O2 -g -Wall" \
>   -DCMAKE_INSTALL_PREFIX=/usr/local

resulsts with the error:

In file included from /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277,
                 from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2868,
                 from /home/primrose/Installed/core/pcu/PCU.h:16,
                 from /home/primrose/Installed/core/apf/apfMesh.cc:8:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function ‘virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)’:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: error: cast between incompatible function types from ‘void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Werror=cast-function-type]
  121 |     (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept,
      |                                              ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:59: error: cast between incompatible function types from ‘void (*)(const void*, void*, int, const MPI::Datatype&)’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Werror=cast-function-type]
  123 |     ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func);
      |                                                           ^~~~
...

Could it be that it does not support MPI 4 but only 3?

primrose@primrose:~/Installed/core/build$ mpiexec --version
mpiexec (OpenRTE) 4.0.3

PCU_Switch_Comm requires valid MPI communicator

We cannot use MPI_UNDEFINED here because PCU requires a valid communicator:

PUMGen/src/input/NetCDFMesh.h

Line 67 in b1661b8

    
           MPI_Comm_split(MPI_COMM_WORLD, (nLocalPart > 0 ? 0 : MPI_UNDEFINED), 0, &commIO);

Replacing MPI_UNDEFINED with 1 should do the trick.

PUMGen fails with MPI abort error

Sun Sep 06 14:01:48, Warn: SimModeler: [433] Code: 60 String: General error
Rank 433 [Sun Sep 6 14:01:48 2020] [c0-3c0s13n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 433
Sun Sep 06 14:01:48, Warn: SimModeler: [966] Code: 60 String: General error
Rank 966 [Sun Sep 6 14:01:48 2020] [c3-3c1s4n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 966
Sun Sep 06 14:01:48, Warn: SimModeler: [984] Code: 60 String: General error
Rank 984 [Sun Sep 6 14:01:48 2020] [c3-3c1s9n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 984
Sun Sep 06 14:01:48, Warn: SimModeler: [688] Code: 60 String: General error
Rank 688 [Sun Sep 6 14:01:48 2020] [c1-3c2s5n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 688
Sun Sep 06 14:01:48, Warn: SimModeler: [856] Code: 60 String: General error
Rank 856 [Sun Sep 6 14:01:48 2020] [c2-3c2s5n0] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 856
Sun Sep 06 14:01:48, Warn: SimModeler: [675] Code: 60 String: General error
Rank 675 [Sun Sep 6 14:01:48 2020] [c1-3c2s2n2] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 675
Sun Sep 06 14:01:48, Warn: SimModeler: [592] Code: 60 String: General error
Rank 592 [Sun Sep 6 14:01:48 2020] [c1-3c0s10n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 592
Sun Sep 06 14:01:48, Warn: SimModeler: [650] Code: 60 String: General error
Rank 650 [Sun Sep 6 14:01:48 2020] [c1-3c1s11n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 650
Sun Sep 06 14:01:48, Warn: SimModeler: [658] Code: 60 String: General error
Rank 658 [Sun Sep 6 14:01:48 2020] [c1-3c1s13n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 658
Sun Sep 06 14:01:48, Warn: SimModeler: [655] Code: 60 String: General error
Rank 655 [Sun Sep 6 14:01:48 2020] [c1-3c1s12n2] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 655
Sun Sep 06 14:01:48, Warn: SimModeler: [668] Code: 60 String: General error
Rank 668 [Sun Sep 6 14:01:48 2020] [c1-3c1s15n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 668
Sun Sep 06 14:01:48, Warn: SimModeler: [667] Code: 60 String: General error
Rank 667 [Sun Sep 6 14:01:48 2020] [c1-3c1s15n2] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 667
Sun Sep 06 14:01:48, Warn: SimModeler: [664] Code: 60 String: General error
Rank 664 [Sun Sep 6 14:01:48 2020] [c1-3c1s14n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 664
Sun Sep 06 14:01:48, Warn: SimModeler: [682] Code: 60 String: General error
Rank 682 [Sun Sep 6 14:01:48 2020] [c1-3c2s4n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 682
Sun Sep 06 14:01:48, Warn: SimModeler: [842] Code: 60 String: General error
Rank 842 [Sun Sep 6 14:01:48 2020] [c2-3c2s1n2] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 842
Sun Sep 06 14:01:48, Warn: SimModeler: [853] Code: 60 String: General error
Rank 853 [Sun Sep 6 14:01:48 2020] [c2-3c2s4n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 853
Sun Sep 06 14:01:48, Warn: SimModeler: [605] Code: 60 String: General error
Sun Sep 06 14:01:48, Warn: SimModeler: [817] Code: 60 String: General error

SIM_PARTITINED_WRAPPER_LIB

Should not default to mpich3

Cf. SIM_LIB in scorec

Apf Missing

Dear All,
I try to compile the new version of PUMGen, However, I got the following error:

-- Cray Programming Environment 2.6.5 C
-- NOTE: LOADEDMODULES changed since initial config!
-- NOTE: this may cause unexpected build errors.
-- Cray Programming Environment 2.6.5 CXX
CMake Warning (dev) at CMakeLists.txt:48 (find_package):
  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  Environment variable HDF5_ROOT is set to:

    /opt/cray/pe/hdf5-parallel/1.10.6.1/INTEL/19.1

  For compatibility, CMake is ignoring the variable.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- HDF5: Using hdf5 compiler wrapper for all C compiling
-- Could NOT find APF (missing: APF_INCLUDE_DIR APF_LIBRARIES) 
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/APF_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/APF_SIM_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/APF_ZOLTAN_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/GMI_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/GMI_SIM_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/LION_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/MA_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/MDS_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/MTH_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/PCU_INCLUDE_DIR
   used as include directory in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
APF_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
APF_SIM_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
APF_ZOLTAN_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
GMI_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
GMI_SIM_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
LION_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
MA_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
MDS_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
MTH_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen
PCU_LIB
    linked by target "pumgen" in directory /project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen

-- Configuring incomplete, errors occurred!
See also "/project/k1488/kadek/myLibs/PUMGen_SeisSol/PUMGen/build/CMakeFiles/CMakeOutput.log".
make: *** No targets specified and no makefile found.  Stop.

Here is my configuration:

mkdir build
cd build
/project/k1488/kadek/myLibs/cmakeSeisSol/bin/cmake/bin/cmake .. -DCMAKE_PREFIX_PATH=/project/k1488/kadek/myLibs/PUMGen_SeisSol/core/:/project/k1488/kadek/myLibs/cmakeSeisSol/lib/:/project/k1488/kadek/myLibs/cmakeSeisSol/bin/:/project/k1488/kadek/myLibs/cmakeSeisSol/include/:/project/k1488/kadek/myLibs/cmakeSeisSol/share/ -DSIMMETRIX=ON \
    -DSIMMETRIX_ROOT=/project/k1488/kadek/myLibs/PUMGen_SeisSol/simmodeler/15.0-210501/ -DSIM_MPI=mpich3 \
    -DCMAKE_BUILD_TYPE=Release\
    -DCMAKE_C_COMPILER=cc -DCMAKE_CXX_COMPILER=CC
make -j 24

I don't understand with the Apf library. Could you please let me know what is wrong with my configuration?

Thank you for your help.

Best regards,
Kadek

Should it be equal to 2?

PUMGen/.clang-format

Line 77 in da94692

IndentWidth: 4

pumgen crashes if properties given by a LayeredModel (VelocityAwareMeshing)

I've noticed that VelocityAwareMeshing seems to always crash with the velocity is given by a LayeredModel.
Here is an extract of the log:

Wed Feb 22 14:42:28, Info:  face id: 116 , MSize = 1000 
Wed Feb 22 14:42:28, Info:  face id: 120 , MSize = 1000 
Wed Feb 22 14:42:28, Info:  face id: 122 , MSize = 1000 
Wed Feb 22 14:42:28, Info:  Enabling velocity aware meshing 
Wed Feb 22 14:42:28, Info:  Gradation rate = 0.8 
Wed Feb 22 14:42:28, Info:  Target equivolume AspectRatio = 12 
Wed Feb 22 14:42:28, Info:  Target equiarea AspectRatio = 6 
Wed Feb 22 14:42:28, Info:  Starting the surface mesher 
Wed Feb 22 14:42:28, Info:  Progress: Surface Meshing 
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 8 with PID 0 on node exception exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

Here is the xml file:

<freeSurface>119</freeSurface>
<!-- hypocenter-->
<boundaryCondition tag="65">121</boundaryCondition>
<!-- fault 7.8-->
<boundaryCondition tag="66">101,107,112,114,121</boundaryCondition>
<!-- fault 7.5-->
<boundaryCondition tag="67">97,109,115,116,120,122</boundaryCondition>
<!-- extras fault 7.8 -->
<boundaryCondition tag="68">110,105</boundaryCondition>
<absorbing>93,95,103,104,108</absorbing>
<surfaceMSize value="1000">101,107,112,114,121,110,105</surfaceMSize>
<surfaceMSize value="1000">97,109,115,116,120,122</surfaceMSize>
<area_AspectRatio value="6"/>
<vol_AspectRatio value="12"/>
<SurfaceMeshing SmoothingLevel="1" SmoothingType="Gradient" DiscreteAngle="15.0" Snap="0"></SurfaceMeshing>
<VolumeMeshing  SmoothingLevel="1" SmoothingType="Gradient" SetOptimisation="1"></VolumeMeshing>
<gradation value="0.8"/>
<globalMSize value="20e3"/>
<VelocityAwareMeshing easiFile="Mw_78_Turkey_rhomulambda1D_Guvercin_et_al.yaml" elementsPerWaveLength="3">
    <VelocityRefinementCuboid frequency="0.1" centerX="0" centerY="0" centerZ="-15e3"
                              halfSizeX="40e10" halfSizeY="15e10" halfSizeZ="15e10" bypassFindRegionAndUseGroup="1"/>
</VelocityAwareMeshing>

and here is the yaml file:

!LayeredModel
  map: !AffineMap
    matrix:
      z1: [0.0, 0.0, 1.0]
    translation:
      z1: 0
  interpolation: lower
  parameters: [rho, mu, lambda, plastCo]
  nodes:
      -1000.0: [2464.9689710139387, 14555395276.94021, 21249511511.522747, 5822158.1107760845]
      -1000000.0: [3400.203751580001, 72261470148.95335, 89717096148.43964, 28904588.059581343]

if I use a LuaMap instead:

!LuaMap
returns: [rho, mu, lambda]
function: |
 function f (x)
    if (x["z"] >= -1000.0) then
      rho = 2464.9689710139387
      mu = 14555395276.94021
      lambda = 21249511511.522747
    elseif (x["z"] >= -1000000.0) then
      rho = 3400.203751580001
      mu = 72261470148.95335
      lambda = 89717096148.43964
    end
   return {
     rho = rho,
     mu = mu,
     lambda = lambda
   }
   end

I'm able to generate the mesh.

the setup is available on exception, at /export/dump/ulrich/PUMGEN_folder/bug_layered_model

installing PUMGen with cmake

Hi,
Today I tried to install PUMGen with cmake.

Do I need to manually set all the pumi/core lib and include path?
APF_SIM_LIB, APF_ZOLTAN_LIB, etc.
Can it be more simple?
When generate with ccmake, I get the following warning:

WARNING: Target "pumgen" requests linking to directory "/hppfs/work/pr45fi/di73yeq4/myLibs/core/lib".  Targets may link only to libraries.  CMake is dropping the item.

does it mean I need to enter the name of each library, e.g. APF_SIM_LIB=/hppfs/work/pr45fi/di73yeq4/myLibs/core/libapf_sim.a

The build fails when linking (maybe related to 2).

Scanning dependencies of target tinyxml2
[  9%] Building CXX object CMakeFiles/tinyxml2.dir/submodules/tinyxml2/tinyxml2.cpp.o
[ 18%] Linking CXX static library libtinyxml2.a
[ 18%] Built target tinyxml2
Scanning dependencies of target pumgen
[ 27%] Building CXX object CMakeFiles/pumgen.dir/src/pumgen.cpp.o
[ 36%] Building CXX object CMakeFiles/pumgen.dir/src/meshreader/FidapReader.cpp.o
[ 45%] Building CXX object CMakeFiles/pumgen.dir/src/meshreader/GambitReader.cpp.o
[ 54%] Building CXX object CMakeFiles/pumgen.dir/src/input/SimModSuite.cpp.o
[ 63%] Building CXX object CMakeFiles/pumgen.dir/src/input/AnalysisAttributes.cpp.o
[ 72%] Building CXX object CMakeFiles/pumgen.dir/src/input/MeshAttributes.cpp.o
[ 81%] Building CXX object CMakeFiles/pumgen.dir/src/input/ParallelVertexFilter.cpp.o
[ 90%] Building CXX object CMakeFiles/pumgen.dir/src/input/split.cpp.o
[100%] Linking CXX executable pumgen
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `SerialMeshFile<puml::ParallelGambitReader>::open(char const*)':
pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x7a): undefined reference to `gmi_register_null'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x84): undefined reference to `gmi_load'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x93): undefined reference to `apf::makeEmptyMdsMesh(gmi_model*, int, bool)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x126): undefined reference to `apf::construct(apf::Mesh2*, int const*, int, int, std::map<int, apf::MeshEntity*, std::less<int>, std::allocator<std::pair<int const, apf::MeshEntity*> > >&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x13c): undefined reference to `apf::alignMdsRemotes(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x145): undefined reference to `apf::deriveMdsModel(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc[_ZN14SerialMeshFileIN4puml20ParallelGambitReaderEE4openEPKc]+0x19a): undefined reference to `apf::setCoords(apf::Mesh2*, double const*, int, std::map<int, apf::MeshEntity*, std::less<int>, std::allocator<std::pair<int const, apf::MeshEntity*> > >&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `ParallelFidapReader::readBoundaries(int*)':
pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x2c): undefined reference to `PCU_Comm_Begin'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x72): undefined reference to `PCU_Comm_Send'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x77): undefined reference to `PCU_Comm_Receive'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x94): undefined reference to `PCU_Comm_Unpack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xbc): undefined reference to `PCU_Comm_Unpack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xdc): undefined reference to `PCU_Comm_Receive'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x6c8): undefined reference to `PCU_Comm_Pack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x6d9): undefined reference to `PCU_Comm_Pack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0x990): undefined reference to `PCU_Comm_Begin'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa10): undefined reference to `PCU_Comm_Pack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa3a): undefined reference to `PCU_Comm_Pack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa51): undefined reference to `PCU_Comm_Send'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa84): undefined reference to `PCU_Comm_Unpack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xa96): undefined reference to `PCU_Comm_Unpack'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN19ParallelFidapReader14readBoundariesEPi[_ZN19ParallelFidapReader14readBoundariesEPi]+0xac1): undefined reference to `PCU_Comm_Receive'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `SerialMeshFile<ParallelFidapReader>::open(char const*)':
pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x7a): undefined reference to `gmi_register_null'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x84): undefined reference to `gmi_load'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x93): undefined reference to `apf::makeEmptyMdsMesh(gmi_model*, int, bool)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x185): undefined reference to `apf::construct(apf::Mesh2*, int const*, int, int, std::map<int, apf::MeshEntity*, std::less<int>, std::allocator<std::pair<int const, apf::MeshEntity*> > >&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x19b): undefined reference to `apf::alignMdsRemotes(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x1a4): undefined reference to `apf::deriveMdsModel(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc[_ZN14SerialMeshFileI19ParallelFidapReaderE4openEPKc]+0x1f9): undefined reference to `apf::setCoords(apf::Mesh2*, double const*, int, std::map<int, apf::MeshEntity*, std::less<int>, std::allocator<std::pair<int const, apf::MeshEntity*> > >&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `main':
pumgen.cpp:(.text.startup+0xa0): undefined reference to `PCU_Comm_Init'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0xfa2): undefined reference to `gmi_register_mesh'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0xfad): undefined reference to `apf::loadMdsMesh(char const*, char const*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0xfe0): undefined reference to `apf::alignMdsMatches(apf::Mesh2*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1079): undefined reference to `PCU_Comm_Self'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x111f): undefined reference to `gmi_write_dmg'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1176): undefined reference to `PCU_Comm_Self'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x11b2): undefined reference to `apf::writeVtkFiles(char const*, apf::Mesh*, int)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x11c1): undefined reference to `apf::countOwned(apf::Mesh*, int, apf::Sharing*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x11cf): undefined reference to `apf::countOwned(apf::Mesh*, int, apf::Sharing*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x12b7): undefined reference to `ma::getInsphere(apf::Mesh2*, apf::MeshEntity*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x13f7): undefined reference to `apf::numberOwnedNodes(apf::Mesh*, char const*, apf::FieldShape*, apf::Sharing*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1404): undefined reference to `apf::makeGlobal(apf::NumberingOf<int>*, bool)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1411): undefined reference to `apf::synchronize(apf::NumberingOf<long>*, apf::Sharing*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1686): undefined reference to `apf::getElementNumbers(apf::NumberingOf<long>*, apf::MeshEntity*, apf::NewArray<long>&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1894): undefined reference to `apf::getSharing(apf::Mesh*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1906): undefined reference to `apf::getNumber(apf::NumberingOf<long>*, apf::Node, int)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x1957): undefined reference to `apf::Mesh::getPoint(apf::MeshEntity*, int, apf::Vector3&)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x286d): undefined reference to `PCU_Comm_Free'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text.startup+0x2985): undefined reference to `gmi_register_null'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: CMakeFiles/pumgen.dir/src/pumgen.cpp.o: in function `SimModSuite::SimModSuite(char const*, char const*, char const*, char const*, char const*, int, char const*, char const*, bool, bool, char const*)':
pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x4ad): undefined reference to `apf::createMesh(PartitionedMesh*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x4b5): undefined reference to `gmi_register_sim()'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x4be): undefined reference to `gmi_import_sim(SGModel*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x506): undefined reference to `apf::createMdsMesh(gmi_model*, apf::Mesh*, bool, bool)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x512): undefined reference to `apf::destroyMesh(apf::Mesh*)'
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: pumgen.cpp:(.text._ZN11SimModSuiteC2EPKcS1_S1_S1_S1_iS1_S1_bbS1_[_ZN11SimModSuiteC5EPKcS1_S1_S1_S1_iS1_S1_bbS1_]+0x564): undefined reference to `apf::Mesh::getModelType(apf::ModelEntity*)'
collect2: error: ld returned 1 exit status
CMakeFiles/pumgen.dir/build.make:211: recipe for target 'pumgen' failed
make[2]: *** [pumgen] Error 1
CMakeFiles/Makefile2:72: recipe for target 'CMakeFiles/pumgen.dir/all' failed
make[1]: *** [CMakeFiles/pumgen.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

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 SIM_PS_KRNL_LIB                  /hppfs/work/pr45fi/di73yeq4/myLibs/SimModelerLib/14.0-190921/lib/x64_rhel6_gcc44/psKrnl/libpskernel.so

Thomas.

.bashrc adjustment for pumgen command

Hi all,
how a .bashrc adjustment should be to make the pumgen command correctly work?
Thanks in advance.

SConstruct in master branch

Dear All,

In the documentation, there is a way to compile with a scons, but there is no SConstruct in the main folder of master branch. Is this scons depreciated?

Thank you.

Best,
Kadek

additional dependencies have been found in case of compilation with intel compiler

Hi all,

So, I was installing PUMGen on my local machine using intel compiler. I found there were similar issues before, for example (from Thomas):
...
H5.c:(.text+0xcb): undefined reference to __intel_sse2_strlen' H5.c:(.text+0x11c): undefined reference to __intel_sse2_strlen'
H5.c:(.text+0x190): undefined reference to __intel_sse2_strlen' H5.c:(.text+0x1e1): undefined reference to __intel_sse2_strlen'
H5.c:(.text+0x27c): undefined reference to `__intel_sse2_strlen'
...

So, I found where the problem was in my case. Basically, a declaration of two libs was missed in SConscript file, namely: irc, svml. Maybe gcc compiler is able to find these libs for itself using the standard lookup paths but intel cannot. I added two lines two SConstruct file:
env.Append(LIBPATH=['<path to my intel installation>/compilers_and_libraries/linux/lib/intel64/'])
env.Append(LIBS=['irc', 'svml']), and I managed to compile PUMGen after that. Basically, hdf5 is looking for these two libs

PUMGEN fails with msh2, floating point exception

I get the following error when running pumgen with this command using a gmsh version 2 file.

pumgen t4.msh2 -s msh2

Tue Aug 02 20:04:58, Info: Using GMSH mesh format 2 (msh2) mesh
Tue Aug 02 20:04:58, Info: Create APF connectivity
Tue Aug 02 20:04:58, Info: Set coordinates in APF
Floating point exception (core dumped)

I attached the msh2 file which should be a valid file (renamed with .txt to allow upload to Github). I generated this file with the Gmsh Python package.

t4.txt

I use the pumgen executable here: /hppfs/work/pr63qo/di73yeq4/myLibs/PUMGen/build/pumgen on SuperMUC-NG.

gmsh2.2 mesh generated on windows cannot be converted

Hi,

I'm collaborating with a windows user and he generated a mesh with gmsh 4.9.? for me.
The mesh cannot be converted with pumgen, which gets stuck.
When generating the mesh on linux, the mesh can easily be converted.
Attached are the geo file and the 2 msh files (we changed the mesh sizes to have a lower cell count).

(base) ulrich@exception:/export/dump/ulrich$ pumgen -s msh2 ExtendedBottom_SeisSol-small_ubuntu.msh 
Wed Mar 15 14:46:49, Info:  Using GMSH mesh format 2 (msh2) mesh 
Wed Mar 15 14:46:49, Info:  Create APF connectivity 
Wed Mar 15 14:46:49, Info:  Set coordinates in APF 
Wed Mar 15 14:46:49, Info:  Mesh size: 22913 
Wed Mar 15 14:46:49, Info:  Minimum insphere found: 0.529276 
Wed Mar 15 14:46:49, Info:  Writing cells 
Wed Mar 15 14:46:49, Info:  Writing vertices 
Wed Mar 15 14:46:49, Info:  Writing group information 
Wed Mar 15 14:46:49, Info:  Writing boundary condition 
Wed Mar 15 14:46:49, Info:  Writing XDMF file 
Wed Mar 15 14:46:49, Info:  Finished successfully 

(base) ulrich@exception:/export/dump/ulrich$ pumgen -s msh2 ExtendedBottom_SeisSol-small_windows.msh 
Wed Mar 15 14:46:57, Info:  Using GMSH mesh format 2 (msh2) mesh

ExtendedBottom_SeisSol-small.zip

Pumgen smooth specific faces

The current pumgen mesh attributes xml has an option of
<SurfaceMeshing SmoothingLevel="3" SmoothingType="Gradient" DiscreteAngle="1.0" Snap="0"/>

Would it be able to specify faces to smooth instead of smoothing all the surfaces in the mesh?

It would be useful to create the complex geometry in most of the subduction zone.

Boundary conditions not detected since new pull request?

I was trying to generate a small Sumatra mesh for debugging purpose.
Below the xml and the log file from pumgen/xml branch.

<freeSurface>25,26,27,29</freeSurface>
<absorbing>18,30</absorbing>
<dynamicRupture>19,20,21,23,24,31,32</dynamicRupture>
<comment text='19,20: forethrust 31,32:Northern BT 23,24: Southern BT 21: Subduction interface'/>
<globalMSize value="100e3"/>
<surfaceMSize value="3000.0">19,20,21,23,24,31,32</surfaceMSize>
<area_AspectRatio value="6"/>
<vol_AspectRatio value="12"/>
<SurfaceMeshing SmoothingLevel="1" SmoothingType="Gradient" DiscreteAngle="15.0" Snap="0"></SurfaceMeshing>
<VolumeMeshing  SmoothingLevel="1" SmoothingType="Gradient" SetOptimisation="1"></VolumeMeshing>
<gradation value="2.0"/>
/var/spool/slurm/job728337/slurm_script: line 43: ulimit: core file size: cannot modify limit: Operation not permitted
Fri Jul 03 10:31:56, Info:  Using SimModSuite
Fri Jul 03 10:31:56, Info:  Loading model
Fri Jul 03 10:32:10, Info:  Extracting cases
Fri Jul 03 10:32:10, Info:  surface smoothing option: surfaceSmoothingLevel surfaceSmoothingType surfaceFaceRotationLimit Snap 1   1   15   0
Fri Jul 03 10:32:10, Info:  volume smoothing option: volumeSmoothingLevel volumrSmoothingType 1   1
Fri Jul 03 10:32:10, Info:  Setting cases
Fri Jul 03 10:32:10, Info:  globalMSize = 100000
Fri Jul 03 10:32:10, Info:  faceid: 19 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info:  faceid: 20 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info:  faceid: 21 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info:  faceid: 23 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info:  faceid: 24 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info:  faceid: 31 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info:  faceid: 32 , surfaceMSize = 3000
Fri Jul 03 10:32:10, Info:  Gradation rate = 2
Fri Jul 03 10:32:10, Info:  Target equivolume AspectRatio = 12
Fri Jul 03 10:32:10, Info:  Target equiarea AspectRatio = 6
Fri Jul 03 10:32:10, Info:  Starting the surface mesher

The following kind of lines are missing:

Tue Mar 24 10:24:24, Info:  faceBound[ 25 ] = 1

problem + solutions compiling pumgen

I had trouble compiling pumgen using mpi.intel/2017 on my desktop.
Basically at linking, I got:

(base) ulrich@tegern:/export/data/ulrich/MyLibs/PUMGen$ mpicxx -o build/pumgen -fopenmp -Wl,-rpath=/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib -Wl,-rpath=/export/data/ulrich/MyLibs/core/build/lib build/src/pumgen.o build/src/input/ParallelVertexFilter.o build/src/meshreader/GambitReader.o build/src/meshreader/FidapReader.o -L/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib -L/export/data/ulrich/MyLibs/core/build/lib -lapf_zoltan -lgmi -lmds -lma -lapf -lpcu -llion -lmth -lhdf5
/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib/libhdf5.a(H5.o): In function `H5_term_library':
H5.c:(.text+0xcb): undefined reference to `__intel_sse2_strlen'
H5.c:(.text+0x11c): undefined reference to `__intel_sse2_strlen'
H5.c:(.text+0x190): undefined reference to `__intel_sse2_strlen'
H5.c:(.text+0x1e1): undefined reference to `__intel_sse2_strlen'
H5.c:(.text+0x27c): undefined reference to `__intel_sse2_strlen'

Which turned out to the fact that mpicxx uses by default g++ and not icpc.

(base) ulrich@tegern:/export/data/ulrich/MyLibs/PUMGen$ mpicxx
This script invokes an appropriate specialized C++ MPI compiler driver.
The following ways (priority order) can be used for changing default
compiler name (g++):
   1. Command line option:  -cxx=<compiler_name>
   2. Environment variable: I_MPI_CXX  (current value '')
   3. Environment variable: MPICH_CXX  (current value '')

therefore I added -cxx=icpc which brought me to the next problem:

(base) ulrich@tegern:/export/data/ulrich/MyLibs/PUMGen$ mpicxx -cxx=icpc -o build/pumgen -fopenmp -Wl,-rpath=/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib -Wl,-rpath=/export/data/ulrich/MyLibs/core/build/lib build/src/pumgen.o build/src/input/ParallelVertexFilter.o build/src/meshreader/GambitReader.o build/src/meshreader/FidapReader.o -L/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib -L/export/data/ulrich/MyLibs/core/build/lib -lapf_zoltan -lgmi -lmds -lma -lapf -lpcu -llion -lmth -lhdf5
/export/data/ulrich/MyLibs/hdf5-1.8.11/build/lib/libhdf5.a(H5Zdeflate.o): In function `H5Z_filter_deflate':
H5Zdeflate.c:(.text+0xcc): undefined reference to `inflateInit_'
H5Zdeflate.c:(.text+0xe2): undefined reference to `inflate'
H5Zdeflate.c:(.text+0x1dd): undefined reference to `compress2'
H5Zdeflate.c:(.text+0x305): undefined reference to `inflateEnd'
H5Zdeflate.c:(.text+0x345): undefined reference to `inflateEnd'
H5Zdeflate.c:(.text+0x39a): undefined reference to `inflateEnd'

Which I solved adding '-lz' to the command

Compiling core on heisenbug

Hi,
I know it is not directly related to PUMGen, but before possibly opening an issue on core, I wanted to get some feedback.
I'm having trouble compiling core on heisenbug (LMU cluster).

module loaded

Currently Loaded Modulefiles:
 1) paraview/5.10.0(default)   2) gcc/10.2.0(default)   3) mpi.ompi/4.1.0(default)

Environment variables:

VERSION="SeisSol-GPU-build"
BASE=/export/dump/ulrich
export SEISSOL_INSTALL_DIR=$BASE/${VERSION}/
export CC=`which mpicc`
#export MPICC=`which mpicc`
export CXX=`which mpiCC`
#export MPICXX=`which mpiCC`
export FC=`which mpif90`

export PATH=$SEISSOL_INSTALL_DIR/bin:$PATH
export LIBRARY_PATH=$SEISSOL_INSTALL_DIR/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=$SEISSOL_INSTALL_DIR/lib:$LD_LIBRARY_PATH
export PKG_CONFIG_PATH=$SEISSOL_INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH
export CMAKE_PREFIX_PATH=$SEISSOL_INSTALL_DIR:$CMAKE_PREFIX_PATH
export CPATH=$SEISSOL_INSTALL_DIR/include:$CPATH
export CPLUS_INCLUDE_PATH=$SEISSOL_INSTALL_DIR/include:$CPLUS_INCLUDE_PATH
export C_INCLUDE_PATH=$SEISSOL_INSTALL_DIR/include:$C_INCLUDE_PATH

export myLibs=/export/dump/ulrich/myLibs/
export path_to_SimModeler=$myLibs/simModelerLib/16.0-220326/
export mpi_name=mpich3
export path_to_pumi=$myLibs/core/
export path_to_SimModeler_lib=$path_to_SimModeler/lib/x64_rhel8_gcc83
export path_to_SimModeler_include_dir=$path_to_SimModeler/include
export path_to_hdf5=/export/dump/ulrich/SeisSol-GPU-build/

compilations process and error:

ulrich@heisenbug:/export/dump/ulrich/myLibs/core$ mkdir build && cd build
ulrich@heisenbug:/export/dump/ulrich/myLibs/core/build$ cmake .. \
>   -DCMAKE_C_COMPILER="`which mpicc`" \
>   -DCMAKE_CXX_COMPILER="`which mpiCC`" \
>   -DSCOREC_EXTRA_C_FLAGS="-O2 -g -Wall" \
>   -DSCOREC_EXTRA_CXX_FLAGS="-O2 -g -Wall" \
>   -DCMAKE_INSTALL_PREFIX=$path_to_pumi \
>   -DENABLE_SIMMETRIX=ON \
>   -DSIM_MPI=$mpi_name \
>   -DSIMMETRIX_LIB_DIR=$path_to_SimModeler_lib \
>   -DSIMMODSUITE_INCLUDE_DIR=$path_to_SimModeler_include_dir
-- The CXX compiler identification is GNU 10.2.0
-- The C compiler identification is GNU 10.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/bin/mpiCC - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- CMAKE_VERSION: 3.18.4
-- SCOREC_VERSION: 2.2.7
-- BUILD_TESTING: OFF
-- CMAKE_INSTALL_PREFIX: /export/dump/ulrich/myLibs/core
-- BUILD_SHARED_LIBS: OFF
-- CMAKE_CXX_FLAGS:  -O2 -g -Werror -Wall -Wextra -Wno-strict-overflow -O2 -g -Wall
-- CMAKE_CXX_FLAGS =  -O2 -g -Werror -Wall -Wextra -Wno-strict-overflow -O2 -g -Wall
-- Try C99 C flag = [ ]
-- Performing Test C99_FLAG_DETECTED
-- Performing Test C99_FLAG_DETECTED - Success
-- CMAKE_C_FLAGS =    -O2 -g -Werror -Wall -Wextra -Wno-strict-overflow -O2 -g -Wall
-- IS_TESTING: OFF
-- MESHES: /export/dump/ulrich/myLibs/core/pumi-meshes
-- BUILD_EXES: ON
-- PUMI_FORTRAN_INTERFACE: OFF
-- PUMI_PYTHON_INTERFACE: OFF
-- MPIRUN: /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/bin/mpirun -np
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot 
-- ENABLE_SIMMETRIX: ON
-- ENABLE_OMEGA_H: OFF
-- ENABLE_FPP: OFF
-- Building with SimModSuite 16.0.220326
-- SIM_ARCHOS x64_rhel8_gcc83
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message):
  The package name passed to `find_package_handle_standard_args`
  (SIMMODSUITE) does not match the name of the calling package (SimModSuite).
  This can lead to problems in calling code that expects `find_package`
  result variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/FindSimModSuite.cmake:177 (find_package_handle_standard_args)
  CMakeLists.txt:114 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found SIMMODSUITE: /export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimPartitionedMesh-mpi.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimDiscrete.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimField.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimAdvMeshing.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimPartitionedMesh-mpi.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimMeshing.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimMeshTools.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimModel.a;/export/dump/ulrich/myLibs/simModelerLib/16.0-220326/lib/x64_rhel8_gcc83/libSimPartitionWrapper-mpich3.a  
-- LION_COMPRESS: OFF
-- PCU_COMPRESS: OFF
-- ENABLE_FIELDSIM: OFF
-- MDS_SET_MAX: 256
-- MDS_ID_TYPE: int
-- ENABLE_ZOLTAN: OFF
-- Looking for clock_gettime
-- Looking for clock_gettime - found
-- ENABLE_STK: OFF
-- ENABLE_STK_MESH: OFF
-- ENABLE_DSP: OFF
-- Looking for mallinfo2
-- Looking for mallinfo2 - not found
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    SCOREC_EXTRA_C_FLAGS


-- Build files have been written to: /export/dump/ulrich/myLibs/core/build
ulrich@heisenbug:/export/dump/ulrich/myLibs/core/build$ make 
Scanning dependencies of target lion
[  1%] Building CXX object lion/CMakeFiles/lion.dir/lionBase64.cc.o
[  1%] Building C object lion/CMakeFiles/lion.dir/lionPrint.c.o
[  1%] Building CXX object lion/CMakeFiles/lion.dir/lionNoZLib.cc.o
[  1%] Linking CXX static library liblion.a
[  1%] Built target lion
Scanning dependencies of target pcu
[  1%] Building C object pcu/CMakeFiles/pcu.dir/pcu.c.o
[  1%] Building C object pcu/CMakeFiles/pcu.dir/pcu_aa.c.o
[  2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_coll.c.o
[  2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_io.c.o
[  2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_buffer.c.o
[  2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_mpi.c.o
[  2%] Building C object pcu/CMakeFiles/pcu.dir/pcu_msg.c.o
[  4%] Building C object pcu/CMakeFiles/pcu.dir/pcu_order.c.o
[  4%] Building C object pcu/CMakeFiles/pcu.dir/pcu_pmpi.c.o
[  4%] Building C object pcu/CMakeFiles/pcu.dir/pcu_util.c.o
[  4%] Building C object pcu/CMakeFiles/pcu.dir/noto/noto_malloc.c.o
[  4%] Building C object pcu/CMakeFiles/pcu.dir/reel/reel.c.o
[  4%] Linking C static library libpcu.a
[  4%] Built target pcu
Scanning dependencies of target gmi
[  4%] Building C object gmi/CMakeFiles/gmi.dir/gmi.c.o
[  4%] Building C object gmi/CMakeFiles/gmi.dir/agm.c.o
[  4%] Building C object gmi/CMakeFiles/gmi.dir/gmi_base.c.o
[  4%] Building C object gmi/CMakeFiles/gmi.dir/gmi_file.c.o
[  5%] Building C object gmi/CMakeFiles/gmi.dir/gmi_lookup.c.o
[  5%] Building C object gmi/CMakeFiles/gmi.dir/gmi_mesh.c.o
[  5%] Building C object gmi/CMakeFiles/gmi.dir/gmi_null.c.o
[  5%] Building C object gmi/CMakeFiles/gmi.dir/gmi_analytic.c.o
[  5%] Linking CXX static library libgmi.a
[  5%] Built target gmi
Scanning dependencies of target gmi_sim
[  6%] Building CXX object gmi_sim/CMakeFiles/gmi_sim.dir/gmi_sim.cc.o
In file included from /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/openmpi/ompi/mpi/cxx/mpicxx.h:277,
                 from /opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/mpi.h:2887,
                 from /export/dump/ulrich/myLibs/core/pcu/PCU.h:16,
                 from /export/dump/ulrich/myLibs/core/gmi_sim/gmi_sim.cc:10:
/opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function ‘virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)’:
/opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/openmpi/ompi/mpi/cxx/op_inln.h:121:25: error: cast between incompatible function types from ‘void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Werror=cast-function-type]
  121 |     (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/software/openmpi/buster/4.1.0_gcc-10.2.0/include/openmpi/ompi/mpi/cxx/op_inln.h:123:38: error: cast between incompatible function types from ‘void (*)(const void*, void*, int, const MPI::Datatype&)’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Werror=cast-function-type]
  123 |     ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func);
      |                                      ^~~~~~~~~~~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
make[2]: *** [gmi_sim/CMakeFiles/gmi_sim.dir/build.make:82: gmi_sim/CMakeFiles/gmi_sim.dir/gmi_sim.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:876: gmi_sim/CMakeFiles/gmi_sim.dir/all] Error 2
make: *** [Makefile:160: all] Error 2

Any idea?

PUMGen compilation and hdf5 on Shaheen

Hii All,

I am getting following error in PUMGen compilation on Shaheen. Any suggestion:

Currently Loaded Modulefiles:

modules/3.2.11.4 12) intel/19.0.5.281 23) alps/6.6.58-7.0.1.1_6.8__g437d88db.ari
craype-haswell 13) python/3.8.0-cdl 24) rca/2.2.20-7.0.1.1_4.51__g8e3fb5b.ari
craype-network-aries 14) cray-libsci/19.06.1 25) atp/3.6.4
craype/2.6.3 15) udreg/2.3.2-7.0.1.1_3.36__g8175d3d.ari 26) perftools-base/7.1.3
cray-mpich/7.7.11 16) ugni/6.0.14.0-7.0.1.1_7.38__ge78e5b0.ari 27) PrgEnv-intel/6.0.5
slurm/slurm 17) pmi/5.0.15 28) cmake/3.13.4
dws/3.0.28-7.0.1.1_6.35__ge55277c.ari 18) dmapp/7.1.1-7.0.1.1_4.52__g38cf134.ari 29) scons/3.0.1
eproxy/2.0.24-7.0.1.1_5.10__g45c478a.ari 19) gni-headers/5.0.12.0-7.0.1.1_6.31__g3b1768f.ari 30) cray-netcdf-hdf5parallel/4.6.3.2
xalt/1.1.2 20) xpmem/2.2.20-7.0.1.1_4.13__g0475745.ari 31) cray-hdf5-parallel/1.10.5.2
darshan/3.1.7 21) job/2.2.4-7.0.1.1_3.40__g36b56f4.ari 32) cray-tpsl/19.06.1
ksl/ksl 22) dvs/2.12_2.2.157-7.0.1.1_9.4__g083131db
simModSuite=yes mpiLib=mpich3 netcdf=yes cc=/opt/cray/pe/craype/2.6.3/bin/cc cxx=/opt/cray/pe/craype/2.6.3/bin/CC logLevel=debug prefixPath=/home/vyasjc/meshing-soft-pumi-pumgen/PUMI/core:/home/vyasjc/meshing-soft-pumi-pumgen/simmetrix/14.0-200719:/home/vyasjc/meshing-soft-pumi-pumgen/parmetis-4.0.3/include:/home/vyasjc/TP-SeisSol/hdf5-1.8.21/build:/home/vyasjc/TP-SeisSol/netcdf-4.6.1/build
scons: Reading SConscript files ...
Checking for C++ library gmi_sim... yes
Checking for C++ library apf_sim... yes
Checking for C++ library apf_zoltan... yes
Checking for C++ library gmi... yes
Checking for C++ library mds... yes
Checking for C++ library ma... yes
Checking for C++ library apf... yes
Checking for C++ library pcu... yes
Checking for C++ library lion... yes
Checking for C++ library mth... yes
Checking whether h5pcc program exists...(cached) yes
IndexError: list index out of range:
File "/home/vyasjc/meshing-soft-pumi-pumgen/PUMGen/SConstruct", line 135:
libs.find(env, 'hdf5', required=True, parallel=True)
File "/home/vyasjc/meshing-soft-pumi-pumgen/PUMGen/site_scons/libs/init.py", line 43:
return lib_find(env, **kw);
File "/home/vyasjc/meshing-soft-pumi-pumgen/PUMGen/site_scons/libs/hdf5.py", line 103:
if not conf.CheckLibWithHeader(flags['LIBS'][0], 'hdf5.h', 'c', extra_libs=flags['LIBS'][1:]):