illinoisrocstar/rocstar-legacy

Rocstar multiphysics simulation application

rocstar-legacy's Issues

"ERROR 1005: Window does not exist" in example simulation

I tried to run the "Rocket Test" in the quick start guide with latest Git master Rocstar, but got a crash once I started the simulation.

mpiexec -n 4 rocstar 
********************************************************************************
*                                                            /\                *
*                                                           //\\               *
*  RRRR    OOOO   CCCC  SSSSS TTTTT   A     RRRR           //  \\              *
*  R   R  O    O C      S       T    A A    R   R         //    \\             *
*  RRRR   O    O C       SSS    T   AAAAA   RRRR         //      \\            *
*  R   R  O    O C          S   T  A     A  R   R       //        \\           *
*  R    R  OOOO   CCCC  SSSSS   T A       A R    R      ============           *
*                                                    _  ============  _        *
*                                                   //\ \\        // /\\       *
* The ROCSTAR multiphysics application is          // \\ \\      // // \\      *
* developed by Illinois Rocstar LLC. You          //   \\ \\    // //   \\     *
* should have received a copy of the             //     \\ \\  // //     \\    *
* Illinois/NCSA Open Source License with        //       \\ \\// //       \\   *
* ROCSTAR. If not, please find it at           //         \\ \/ //         \\  *
* http://opensource.org/licenses/NCSA.        ++++++++++++++++++++++++++++++++ *
*                                                                              *
*        Copyright (C) 2015 Illinois Rocstar LLC. All rights reserved.         *
*                                                                              *
********************************************************************************

Rocflu:
Rocflu: =======================================
Rocflu:                                        
Rocflu:                RocfluidMP              
Rocflu:                                        
Rocflu: Copyright (C) 2015 Illinois Rocstar LLC.
Rocflu:                                        
Rocflu: =======================================
Rocflu:
Rocflu:
Rocflu: Reading user input file...
Rocflu:
Rocflu: Reading Rocflu boundary condition file...
Rocmop: Warning: Could not open configfile, Rocmop/RocmopControl.txt.

Roccom:Roccom: ERROR 1005: Window does not exist
Roccom: Error encountered when processing fluidSurfIn
Roccom: In Roccom_base::get_window of file /Volumes/Storage/rocstar/ROcstar/Roccom/src/Roccom_base.C at line 2171
Roccom: In Roccom_base::get_size of file /Volumes/Storage/rocstar/ROcstar/Roccom/src/Roccom_base.C at line 1005
Roccom: When processing attribute fluidSurfIn.nc
terminate called after throwing an instance of 'COM::Error_code'
[Jamies-Mac-Pro:05549] *** Process received signal ***
[Jamies-Mac-Pro:05549] Signal: Abort trap: 6 (6)
[Jamies-Mac-Pro:05549] Signal code:  (0)
[Jamies-Mac-Pro:05549] [ 0] 0   libsystem_platform.dylib            0x00007fff8d81c5aa _sigtramp + 26
[Jamies-Mac-Pro:05549] [ 1] 0   ???                                 0x0000000000000000 0x0 + 0
[Jamies-Mac-Pro:05549] [ 2] 0   libsystem_c.dylib                   0x00007fff87f37bba abort + 125
[Jamies-Mac-Pro:05549] [ 3] 0   libstdc++.6.dylib                   0x000000010d9306c4 _ZN9__gnu_cxx27__verbose_terminate_handlerEv + 276
[Jamies-Mac-Pro:05549] *** End of error message ***

Roccom:Roccom: ERROR 1005: Window does not exist
Roccom: Error encountered when processing fluidSurfIn
Roccom: In Roccom_base::get_window of file /Volumes/Storage/rocstar/ROcstar/Roccom/src/Roccom_base.C at line 2171
Roccom: In Roccom_base::get_size of file /Volumes/Storage/rocstar/ROcstar/Roccom/src/Roccom_base.C at line 1005
Roccom: When processing attribute fluidSurfIn.nc
terminate called after throwing an instance of 'COM::Error_code'
[Jamies-Mac-Pro:05550] *** Process received signal ***
[Jamies-Mac-Pro:05550] Signal: Abort trap: 6 (6)
[Jamies-Mac-Pro:05550] Signal code:  (0)
[Jamies-Mac-Pro:05550] [ 0] 0   libsystem_platform.dylib            0x00007fff8d81c5aa _sigtramp + 26
[Jamies-Mac-Pro:05550] [ 1] 0   ???                                 0x0000000000000000 0x0 + 0
[Jamies-Mac-Pro:05550] [ 2] 0   libsystem_c.dylib                   0x00007fff87f37bba abort + 125
[Jamies-Mac-Pro:05550] [ 3] 0   libstdc++.6.dylib                   0x00000001102ee6c4 _ZN9__gnu_cxx27__verbose_terminate_handlerEv + 276
[Jamies-Mac-Pro:05550] *** End of error message ***

Roccom:Roccom: ERROR 1005: Window does not exist
Roccom: Error encountered when processing fluidSurfIn
Roccom: In Roccom_base::get_window of file /Volumes/Storage/rocstar/ROcstar/Roccom/src/Roccom_base.C at line 2171
Roccom: In Roccom_base::get_size of file /Volumes/Storage/rocstar/ROcstar/Roccom/src/Roccom_base.C at line 1005
Roccom: When processing attribute fluidSurfIn.nc
terminate called after throwing an instance of 'COM::Error_code'
[Jamies-Mac-Pro:05551] *** Process received signal ***
[Jamies-Mac-Pro:05551] Signal: Abort trap: 6 (6)
[Jamies-Mac-Pro:05551] Signal code:  (0)
[Jamies-Mac-Pro:05551] [ 0] 0   libsystem_platform.dylib            0x00007fff8d81c5aa _sigtramp + 26
[Jamies-Mac-Pro:05551] [ 1] 0   ???                                 0x0000000000000000 0x0 + 0
[Jamies-Mac-Pro:05551] [ 2] 0   libsystem_c.dylib                   0x00007fff87f37bba abort + 125
[Jamies-Mac-Pro:05551] [ 3] 0   libstdc++.6.dylib                   0x000000010cce96c4 _ZN9__gnu_cxx27__verbose_terminate_handlerEv + 276
[Jamies-Mac-Pro:05551] *** End of error message ***

Roccom:Roccom: ERROR 1005: Window does not exist
Roccom: Error encountered when processing fluidSurfIn
Roccom: In Roccom_base::get_window of file /Volumes/Storage/rocstar/ROcstar/Roccom/src/Roccom_base.C at line 2171
Roccom: In Roccom_base::get_size of file /Volumes/Storage/rocstar/ROcstar/Roccom/src/Roccom_base.C at line 1005
Roccom: When processing attribute fluidSurfIn.nc
terminate called after throwing an instance of 'COM::Error_code'
[Jamies-Mac-Pro:05552] *** Process received signal ***
[Jamies-Mac-Pro:05552] Signal: Abort trap: 6 (6)
[Jamies-Mac-Pro:05552] Signal code:  (0)
[Jamies-Mac-Pro:05552] [ 0] 0   libsystem_platform.dylib            0x00007fff8d81c5aa _sigtramp + 26
[Jamies-Mac-Pro:05552] [ 1] 0   ???                                 0x0000000000000000 0x0 + 0
[Jamies-Mac-Pro:05552] [ 2] 0   libsystem_c.dylib                   0x00007fff87f37bba abort + 125
[Jamies-Mac-Pro:05552] [ 3] 0   libstdc++.6.dylib                   0x000000011028b6c4 _ZN9__gnu_cxx27__verbose_terminate_handlerEv + 276
[Jamies-Mac-Pro:05552] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 2 with PID 0 on node Jamies-Mac-Pro exited on signal 6 (Abort trap: 6).
--------------------------------------------------------------------------

I am on an OS X 10.9 virtual machine with GCC 7.1.0 and open-mpi installed through Homebrew.

Interestingly enough, if I just run the rocprep and rocstar commands, without changing the FluidModule to Rocflu, it works fine with no crash.

Questions about unstructured grid format

I want to know what are the unstructured grid formats that Rocstar supports.
I used ICEM to output the grid, but I didn't find the right format

Looking forward to your reply. Thank you

MPI error in running rocstar

When I execute the following script:
rflupart -c ACM -v 2
The error message appears as follows:
*** The MPI_Comm_f2c() function was called before MPI_INIT was invoked. *** This is disallowed by the MPI standard. *** Your MPI job will now abort.

The compiler and software versions I use are:
"-- The CXX compiler identification is GNU 4.8.5
-- The C compiler identification is GNU 4.8.5
-- The Fortran compiler identification is GNU 4.8.5
-- Found MPI_C: /usr/local/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/local/lib/libmpi.so (found version "3.1")
-- Found MPI_Fortran: /usr/local/lib/libmpi_usempi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")"

The openmpi version I installed is 4.0.4, but the version cmake prompts is 3.1. I don't know why

Hope to get help from developers, thank you very much

Module integrity issues

Does anyone compile particles module successfully? This module does not compiled as a part of Rocstar!!

Memory Issue with Rocstar v1.0

We are having a memory issue running Rocstar v1.0. While running the ACM test case with either Rocflu or Rocflo, Rocstar's memory usage continues to increase until the memory is filled and the solver crashes. This memory leak has been verified on two different systems: one, a high end Dell CFD Workstation running Redhat Enterprise v7.2, and two, a laptop running Ubuntu 14.04 LTS.

The two builds of Rocstar were used to solve the same Rocflu ACM test case with 4 processors. The used memory for each simulation was charted as a function of time and the rate of memory increase is identical between the two systems. See the attached PDF containing the plots.

Comparison of Rocstar Runs.pdf

Included in the plots are information about the Third Party Libraries and compilers used for preparing

This problem appears to be limited to when the Rocburn module is called - all of the other test cases, Super Seismic Shock, Elastic Piston, and the Shock Panel do not exhibit the memory leak. When the same Rocflu ACM test case was prepared WITHOUT including the '-b' in Rocprep, it also did not suffer from the memory leak.

Please let me know if there is any other information I need to supply in order to help resolve this issue.

Thank you.

cmake error

I downloaded Rocstar-legacy file and followed the instruction in RocstarQuickStart, downloaded all the required tpl and set all the environment variables, and I typed:

cmake $ROCSTAR_SOURCE

error occurred:

CMake Error at CMakeLists.txt:31 (add_subdirectory):
  The source directory

    /usr/local/src/Rocstar-legacy-master/IRAD

  does not contain a CMakeLists.txt file.


-- A library with BLAS API found.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
CMake Error at CMakeLists.txt:97 (MESSAGE):
  Doxygen is needed to build the documentation.


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:
HDF5_LIB

However, I installed libhdf5-dev but the cmake error still saying HDF5_LIB cannot be founded.
The Doxygen site http://illinoisrocstar.github.io/Rocstar/ also cannot be found, site not founded 404.
According to IRAD, IRAD file in Rocstar-legacy is empty, I downloaded IRAD file in IRAD-master and copy it to Rocstar-legacy/IRAD and cmake, the error occurs:

-- No build type selected, default to Release
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
CMake Error at IRAD/CMakeLists.txt:74 (MESSAGE):
  Doxygen is needed to build the documentation.


-- Configuring incomplete, errors occurred!
See also "/usr/local/src/Rocstar-legacy-master/CMakeFiles/CMakeOutput.log".
See also "/usr/local/src/Rocstar-legacy-master/CMakeFiles/CMakeError.log".

It seems that I need to download Doxygen file in http://illinoisrocstar.github.io/Rocstar/, but the site cannot be found.

Build error: unknown type 'uint'

I get this error when building with both OS X and Windows (MinGW):

[ 52%] Built target Rocprop
[ 52%] Building Fortran object RocfluidMP/Rocflo/CMakeFiles/Rocflo.dir/RFLO_C2eAvgCoeffs.F90.o
In file included from /Volumes/Storage/rocstar/ROcstar/Rocmop/src/Rocmop_1.C:46:0:
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:526:25: error: expected ')' before 'size'
   MyEntityIterator(uint size){ _cur = 1; _size = size;}
                         ^~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:562:3: error: 'uint' does not name a type; did you mean 'rint'?
   uint  _cur; // The current node's position.
   ^~~~
   rint
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:563:3: error: 'uint' does not name a type; did you mean 'rint'?
   uint  _size;// The size of the element array
   ^~~~
   rint
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h: In destructor 'virtual Mesquite::MyEntityIterator::~MyEntityIterator()':
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:530:4: error: '_cur' was not declared in this scope
   {_cur = 0;
    ^~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:531:5: error: '_size' was not declared in this scope
     _size = 0;
     ^~~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h: In member function 'virtual void Mesquite::MyEntityIterator::restart()':
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:536:5: error: '_cur' was not declared in this scope
     _cur = 1;
     ^~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h: In member function 'virtual void* Mesquite::MyEntityIterator::operator*() const':
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:541:9: error: '_cur' was not declared in this scope
     if (_cur > _size)
         ^~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:541:16: error: '_size' was not declared in this scope
     if (_cur > _size)
                ^~~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h: In member function 'virtual void Mesquite::MyEntityIterator::operator++()':
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:549:5: error: '_cur' was not declared in this scope
     _cur ++;
     ^~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h: In member function 'virtual bool Mesquite::MyEntityIterator::is_at_end() const':
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:558:9: error: '_cur' was not declared in this scope
     if (_cur <= _size) return 0;
         ^~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/include/MesqPane_95.h:558:17: error: '_size' was not declared in this scope
     if (_cur <= _size) return 0;
                 ^~~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/src/Rocmop_1.C: In member function 'void MOP::Rocmop::perturb_stationary()':
/Volumes/Storage/rocstar/ROcstar/Rocmop/src/Rocmop_1.C:1726:6: error: 'uint' was not declared in this scope
  for(uint k=0, nk=elist.size(); k<nk; ++k){
      ^~~~
/Volumes/Storage/rocstar/ROcstar/Rocmop/src/Rocmop_1.C:1726:6: note: suggested alternative: 'rint'
  for(uint k=0, nk=elist.size(); k<nk; ++k){
      ^~~~
      rint
/Volumes/Storage/rocstar/ROcstar/Rocmop/src/Rocmop_1.C:1726:33: error: 'k' was not declared in this scope
  for(uint k=0, nk=elist.size(); k<nk; ++k){
                                 ^
/Volumes/Storage/rocstar/ROcstar/Rocmop/src/Rocmop_1.C:1726:35: error: 'nk' was not declared in this scope
  for(uint k=0, nk=elist.size(); k<nk; ++k){
                                   ^~
/Volumes/Storage/rocstar/ROcstar/Rocmop/src/Rocmop_1.C:1726:35: note: suggested alternative: 'nj'
  for(uint k=0, nk=elist.size(); k<nk; ++k){
                                   ^~
                                   nj

It looks like several files try to use some sort of 'uint' type, but that isn't in the standard library so the build dies. I was able to fix it by replacing all instances of uint with unsigned int:

find Rocmop -name '*.C' -exec sed -i '' -e 's/uint/unsigned int/g' {} \;