Enable particle input from file #33

diehlpk · 2023-07-27T20:23:33Z

Attempt to read particles from a CSV file.

Closes #9

Update CMakeLists.txt

streeve · 2023-08-08T21:58:20Z

Updated here now that the crack branching problem is merged; also split into a new example to separate the specific file format from the source

diehlpk · 2023-08-31T04:13:45Z

@streeve I tried to compile the new version of the example.

I added the example to CMake to finally compile it
I fixed some of the C++ compiler errors for reading the CSV file

However, I get some Kokkos errors while compiling.

/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp: In function ‘void read_particles(std::__cxx11::string, ParticleType&)’:
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:56:14: error: there are no arguments to ‘slice_v’ that depend on a template parameter, so a declaration of ‘slice_v’ must be available [-fpermissive]
     auto v = slice_v();
              ^~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:56:14: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:57:14: error: there are no arguments to ‘slice_f’ that depend on a template parameter, so a declaration of ‘slice_f’ must be available [-fpermissive]
     auto f = slice_f();
              ^~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:58:17: error: there are no arguments to ‘slice_type’ that depend on a template parameter, so a declaration of ‘slice_type’ must be available [-fpermissive]
     auto type = slice_type();
                 ^~~~~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:59:16: error: there are no arguments to ‘slice_rho’ that depend on a template parameter, so a declaration of ‘slice_rho’ must be available [-fpermissive]
     auto rho = slice_rho();
                ^~~~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:60:14: error: there are no arguments to ‘slice_u’ that depend on a template parameter, so a declaration of ‘slice_u’ must be available [-fpermissive]
     auto u = slice_u();
              ^~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:61:19: error: there are no arguments to ‘slice_nofail’ that depend on a template parameter, so a declaration of ‘slice_nofail’ must be available [-fpermissive]
     auto nofail = slice_nofail();
                   ^~~~~~~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:66:41: error: expected primary-expression before ‘policy’
         Kokkos::RangePolicy<exec_space> policy( 0, x.size() ),
                                         ^~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp: In lambda function:
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:69:19: error: ‘pid’ was not declared in this scope
             pvol( pid ) = vol( i );
                   ^~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp: In function ‘int main(int, char**)’:
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:159:19: error: ‘class std::shared_ptr<CabanaPD::Particles<Kokkos::Device<Kokkos::Serial, Kokkos::HostSpace>, CabanaPD::PMB> >’ has no member named ‘update_after_read’
         particles.update_after_read( exec_space(), halo_width, num_cell );
                   ^~~~~~~~~~~~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp: In instantiation of ‘void read_particles(std::__cxx11::string, ParticleType&) [with ParticleType = std::shared_ptr<CabanaPD::Particles<Kokkos::Device<Kokkos::Serial, Kokkos::HostSpace>, CabanaPD::PMB> >; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:157:46:   required from here
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:49:61: error: no type named ‘memory_space’ in ‘class std::shared_ptr<CabanaPD::Particles<Kokkos::Device<Kokkos::Serial, Kokkos::HostSpace>, CabanaPD::PMB> >’
     using memory_space = typename ParticleType::memory_space;
                                                             ^
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:54:25: error: ‘class std::shared_ptr<CabanaPD::Particles<Kokkos::Device<Kokkos::Serial, Kokkos::HostSpace>, CabanaPD::PMB> >’ has no member named ‘slice_x’
     auto px = particles.slice_x();
               ~~~~~~~~~~^~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:55:27: error: ‘class std::shared_ptr<CabanaPD::Particles<Kokkos::Device<Kokkos::Serial, Kokkos::HostSpace>, CabanaPD::PMB> >’ has no member named ‘slice_vol’
     auto pvol = particles.slice_vol();
                 ~~~~~~~~~~^~~~~~~~~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:56:21: error: ‘slice_v’ was not declared in this scope
     auto v = slice_v();
              ~~~~~~~^~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:56:21: note: suggested alternative: ‘ssize_t’
     auto v = slice_v();
              ~~~~~~~^~
              ssize_t
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:57:21: error: ‘slice_f’ was not declared in this scope
     auto f = slice_f();
              ~~~~~~~^~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:57:21: note: suggested alternative: ‘ssize_t’
     auto f = slice_f();
              ~~~~~~~^~
              ssize_t
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:58:27: error: ‘slice_type’ was not declared in this scope
     auto type = slice_type();
                 ~~~~~~~~~~^~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:58:27: note: suggested alternative: ‘H5Rget_type’
     auto type = slice_type();
                 ~~~~~~~~~~^~
                 H5Rget_type
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:59:25: error: ‘slice_rho’ was not declared in this scope
     auto rho = slice_rho();
                ~~~~~~~~~^~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:60:21: error: ‘slice_u’ was not declared in this scope
     auto u = slice_u();
              ~~~~~~~^~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:60:21: note: suggested alternative: ‘ssize_t’
     auto u = slice_u();
              ~~~~~~~^~
              ssize_t
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:61:31: error: ‘slice_nofail’ was not declared in this scope
     auto nofail = slice_nofail();
                   ~~~~~~~~~~~~^~
/home/diehlpk/Compile/CabanaPD/examples/read_file.cpp:61:31: note: suggested alternative: ‘nofail’
     auto nofail = slice_nofail();
                   ~~~~~~~~~~~~^~

Could you please have a look?

examples/read_file.cpp

streeve · 2023-08-31T15:16:47Z

@diehlpk I fixed the compilation locally - should be much more usable now

diehlpk · 2023-08-31T15:57:22Z

@streeve thanks, I will compile and test a uniform bar.

diehlpk · 2023-09-01T08:18:41Z

@streeve

I get now a new error which was not there before:

In file included from /home/diehlpk/Compile/CabanaPD/src/CabanaPD.hpp:16,
                 from /home/diehlpk/Compile/CabanaPD/examples/elastic_wave.cpp:19:
/home/diehlpk/Compile/CabanaPD/src/CabanaPD_Comm.hpp: In member function ‘void CabanaPD::HaloIds<LocalGridType, PositionSliceType>::build(const LocalGridType&)’:
/home/diehlpk/Compile/CabanaPD/src/CabanaPD_Comm.hpp:114:33: error: ‘getTopology’ is not a member of ‘Cajita’
         auto topology = Cajita::getTopology( local_grid );
                                 ^~~~~~~~~~~
/home/diehlpk/Compile/CabanaPD/src/CabanaPD_Comm.hpp:114:33: note: suggested alternative:
In file included from /home/diehlpk/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/cabana-master-35llli4s5ak7e2at4sxta22swwr6ydzb/include/Cajita.hpp:34,
                 from /home/diehlpk/Compile/CabanaPD/src/CabanaPD_Boundary.hpp:18,
                 from /home/diehlpk/Compile/CabanaPD/src/CabanaPD.hpp:15,
                 from /home/diehlpk/Compile/CabanaPD/examples/elastic_wave.cpp:19:
/home/diehlpk/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/cabana-master-35llli4s5ak7e2at4sxta22swwr6ydzb/include/Cajita_ParticleGridDistributor.hpp:57:1: note:   ‘Cajita::Impl::getTopology’
 getTopology( const LocalGridType& local_grid )
 ^~~~~~~~~~~
In file included from /home/diehlpk/Compile/CabanaPD/src/CabanaPD.hpp:16,
                 from /home/diehlpk/Compile/CabanaPD/examples/elastic_wave.cpp:19:
/home/diehlpk/Compile/CabanaPD/src/CabanaPD_Comm.hpp:115:40: error: ‘getUniqueTopology’ is not a member of ‘Cabana’
         auto unique_topology = Cabana::getUniqueTopology(
                                        ^~~~~~~~~~~~~~~~~
/home/diehlpk/Compile/CabanaPD/src/CabanaPD_Comm.hpp:115:40: note: suggested alternative:
In file included from /home/diehlpk/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/cabana-master-35llli4s5ak7e2at4sxta22swwr6ydzb/include/Cabana_Distributor.hpp:20,
                 from /home/diehlpk/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/cabana-master-35llli4s5ak7e2at4sxta22swwr6ydzb/include/Cabana_Core.hpp:40,
                 from /home/diehlpk/Compile/CabanaPD/src/CabanaPD_Boundary.hpp:17,
                 from /home/diehlpk/Compile/CabanaPD/src/CabanaPD.hpp:15,
                 from /home/diehlpk/Compile/CabanaPD/examples/elastic_wave.cpp:19:
/home/diehlpk/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/cabana-master-35llli4s5ak7e2at4sxta22swwr6ydzb/include/Cabana_CommunicationPlan.hpp:360:25 note:   ‘Cabana::Impl::getUniqueTopology’
 inline std::vector<int> getUniqueTopology( MPI_Comm comm,
                         ^~~~~~~~~~~~~~~~~
In file included from /home/diehlpk/Compile/CabanaPD/src/CabanaPD.hpp:16,
                 from /home/diehlpk/Compile/CabanaPD/examples/elastic_wave.cpp:19:
/home/diehlpk/Compile/CabanaPD/src/CabanaPD_Comm.hpp: In constructor ‘CabanaPD::Comm<ParticleType, CabanaPD::PMB>::Comm(ParticleType&, int)’:
/home/diehlpk/Compile/CabanaPD/src/CabanaPD_Comm.hpp:207:33: error: ‘getTopology’ is not a member of ‘Cajita’
         auto topology = Cajita::getTopology( *local_grid );
                                 ^~~~~~~~~~~
/home/diehlpk/Compile/CabanaPD/src/CabanaPD_Comm.hpp:207:33: note: suggested alternative:
In file included from /home/diehlpk/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/cabana-master-35llli4s5ak7e2at4sxta22swwr6ydzb/include/Cajita.hpp:34,
                 from /home/diehlpk/Compile/CabanaPD/src/CabanaPD_Boundary.hpp:18,
                 from /home/diehlpk/Compile/CabanaPD/src/CabanaPD.hpp:15,
                 from /home/diehlpk/Compile/CabanaPD/examples/elastic_wave.cpp:19:
/home/diehlpk/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/cabana-master-35llli4s5ak7e2at4sxta22swwr6ydzb/include/Cajita_ParticleGridDistributor.hpp:57:1: note:   ‘Cajita::Impl::getTopology’
 getTopology( const LocalGridType& local_grid )
 ^~~~~~~~~~~
make[2]: *** [examples/CMakeFiles/ElasticWave.dir/build.make:76: examples/CMakeFiles/ElasticWave.dir/elastic_wave.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:175: examples/CMakeFiles/ElasticWave.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

streeve · 2023-09-01T13:40:14Z

Sorry, I forgot to say you'll need to update to the latest Cabana master (readme has been updated with the minimum commit necessary)

diehlpk · 2023-09-04T09:08:22Z

@streeve The code compiles now, but we get a segmentation fault after reading the CSV file.

I nailed it down between

CabanaPD/examples/read_file.cpp

Line 43 in 8fb8f42

// Create unmanaged Views in order to copy to device.

a and

CabanaPD/examples/read_file.cpp

Line 84 in 8fb8f42

}

.

Here is the output:

[rostam1:3546840] *** Process received signal ***
[rostam1:3546840] Signal: Segmentation fault (11)
[rostam1:3546840] Signal code: Address not mapped (1)
[rostam1:3546840] Failing at address: (nil)
[rostam1:3546840] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f5291425cf0]
[rostam1:3546840] [ 1] ./examples/ReadFile[0x416c0b]
[rostam1:3546840] [ 2] ./examples/ReadFile[0x407a39]
[rostam1:3546840] [ 3] /lib64/libc.so.6(__libc_start_main+0xe5)[0x7f5291088d85]
[rostam1:3546840] [ 4] ./examples/ReadFile[0x408b5e]
[rostam1:3546840] *** End of error message ***
Segmentation fault (core dumped)

and with gdb, we get

 Thread 1 "ReadFile" received signal SIGSEGV, Segmentation fault.
0x0000000000416c0b in void read_particles<CabanaPD::Particles<Kokkos::Device<Kokkos::Serial, Kokkos::HostSpace>, CabanaPD::PMB, 3> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, CabanaPD::Particles<Kokkos::Device<Kokkos::Serial, Kokkos::HostSpace>, CabanaPD::PMB, 3>&) ()
Missing separate debuginfos, use: yum debuginfo-install libgcc-8.5.0-18.el8.x86_64 libstdc++-8.5.0-18.el8.x86_64 munge-libs-0.5.13-2.el8.x86_64

I am attending a conference this week and just had a few minutes to test things. I can have a more detailed look next week.

streeve · 2023-09-05T14:26:35Z

If you attach an example file I can test as well

diehlpk · 2023-09-19T15:18:06Z

This is the CSV file easy.csv and the image of the corresponding mesh

streeve · 2023-09-28T22:13:06Z

@diehlpk as you can see from the last commit, there were a lot of necessary changes. Runs for me now locally

diehlpk · 2023-09-28T22:16:54Z

@streeve thanks. I will try to run a larger geometry and apply the boundary conditions.

streeve · 2023-10-27T19:54:08Z

To do:

Generalize boundary for fields other than forces
Remove dx (build a grid with the cutoff distance and fix halo=1)

streeve · 2023-11-01T18:37:47Z

@diehlpk made the changes we discussed - let me know if you have any issues or if you have larger files for me to test with

diehlpk · 2023-11-01T21:20:28Z

@streeve thanks, I will upload the coarsest grid, we used in the previous simulations this evening.

diehlpk · 2023-11-02T02:09:39Z

@streeve Please find attached a mesh more suitable for the comparison with the experiment.

Here is the file astm-d638.csv

If that mesh works, we would be good to setup the experimet.

diehlpk · 2023-11-02T02:17:59Z

@streeve mayve we should add a very small CSV file to the repo to execute the example. What do you think?

issues with LinkedCellList (in VerletList) with single bin in a given dimension

streeve · 2023-11-07T16:54:55Z

mayve we should add a very small CSV file to the repo to execute the example. What do you think?

I'm okay with that as long as it's very small (a dog-bone with 100s of particles would be nice)

streeve · 2023-11-07T16:56:14Z

I ran with the astm file and can correctly create the BC we want, but I'm not sure if the issues I see locally are because of input magnitudes or a bug

streeve · 2023-11-10T14:44:11Z

@diehlpk should be ready to test. The last commit adds the linear ramp for BC (as well as the option to turn off the BC at some point in the simulation). I also had to remove some duplicate positions with the test mesh I was using

streeve · 2023-11-14T20:42:46Z

@diehlpk let me know if you notice any issues - I can try to fix before we meet next

diehlpk · 2023-11-15T22:33:48Z

@streeve I was attending SC. I will testbit before the meeting back home.

diehlpk · 2023-11-29T03:50:00Z

@streeve I prepared a 3D mesh and uploaded the mesh to the shared folder.

I will try this week to setup the 2d case with the experimental data.

Could you please try the 3d mesh?

diehlpk and others added 3 commits May 22, 2023 22:21

Merge pull request #1 from diehlpk/diehlpk-patch-1

bc3d24f

Update CMakeLists.txt

Merge branch 'main' into crack_branching

fb39ede

add function to read csv files

3d35944

streeve changed the title ~~Crack branching~~ Crack branching with file input Jul 27, 2023

diehlpk mentioned this pull request Jul 27, 2023

Read particles from file #9

Open

2 tasks

streeve added 3 commits July 27, 2023 17:21

format

5f6984e

Move csv read to example file; update after read

80c1dee

Merge branch 'main' into file_read

3eaac53

diehlpk added 2 commits August 30, 2023 23:07

Add read file example to CMake

2137af1

Fix some C++ compiler errors related to tread the CSV file

181608a

streeve reviewed Aug 31, 2023

View reviewed changes

examples/read_file.cpp Outdated Show resolved Hide resolved

streeve added 3 commits August 31, 2023 11:03

Merge branch 'main' into file_read

d9d4a53

fixup: type mistake

4eadd51

fixup: file read example compilation

d464f37

Merge branch 'ORNL:main' into crack_branching

8fb8f42

streeve added 3 commits September 23, 2023 16:10

Merge branch 'main' into file_read

185d528

fixup: function rename

2d04d49

fixup: file read and example details

ade2d1b

streeve mentioned this pull request Sep 28, 2023

Enable variable dimension (2d/3d) #58

Merged

streeve added 2 commits October 16, 2023 08:51

fixup: assert BC plane inputs are reasonable

5671fac

fixup: file read inputs

e005fa1

streeve added 3 commits October 30, 2023 16:48

fixup: allow displacement BC

fab6caa

fixup: remove dx for file reads

773c3a5

fixup: force non-zero extent for pseudo-2d

905ae39

streeve changed the title ~~Crack branching with file input~~ Enable particle input from file Nov 1, 2023

Merge branch 'main' into file_read

fb4906d

streeve added 5 commits November 2, 2023 12:19

fixup: memory space vs device type

317abcd

fixup: BC regions

22245d9

Switch back to dx;

bb1512c

issues with LinkedCellList (in VerletList) with single bin in a given dimension

fixup: force BC changed to displacement

45bd868

Add no-fail region

4e6eb1a

streeve added 3 commits November 10, 2023 07:04

Add split values for symmetric BC

77b2196

Guard against duplicate points in file reading

d47622e

Add time dependent BC with linear ramp

ab6f3e5

streeve force-pushed the crack_branching branch from e51430a to ab6f3e5 Compare November 10, 2023 14:43

streeve added 2 commits November 10, 2023 12:21

fixup: file read abs()

e4107f8

Update HIP CI version

89c9e6c

streeve force-pushed the crack_branching branch from 3978b6c to 89c9e6c Compare November 10, 2023 17:46

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Enable particle input from file #33

Enable particle input from file #33

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Enable particle input from file #33

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Enable particle input from file #33

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