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Dependency Bump #66

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merged 10 commits into from
Sep 5, 2024
Merged

Dependency Bump #66

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7da8636
Dependency Bump
Joroks Sep 3, 2024
147c015
Dependency Bump
Joroks Sep 3, 2024
7ba920d
Test for MPI
Joroks Sep 3, 2024
04ae5c1
Ignore local preferences
Joroks Sep 4, 2024
6a5a3ac
Check config on startup
Joroks Sep 4, 2024
05f244c
regenerate api.jl
Joroks Sep 4, 2024
643efca
Dependency Bump
Joroks Sep 4, 2024
9341c86
Merge branch 'dep_bump' of github.com:Joroks/LAMMPS.jl into dep_bump
Joroks Sep 4, 2024
8b6bb40
Fail test, if MPI is not enabled
Joroks Sep 4, 2024
85bb97c
fix mpitest
Joroks Sep 4, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
*.jl.mem

Manifest.toml
LocalPreferences.toml

# generated docs
docs/build/
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2 changes: 1 addition & 1 deletion Project.toml
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Expand Up @@ -12,7 +12,7 @@ MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"

[compat]
CEnum = "0.4, 0.5"
LAMMPS_jll = "2.5"
LAMMPS_jll = "2.6.0"
Preferences = "1"
MPI = "0.20"
julia = "1.8"
22 changes: 11 additions & 11 deletions res/Manifest.toml
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Expand Up @@ -17,7 +17,7 @@ version = "0.5.0"

[[Clang]]
deps = ["CEnum", "Clang_jll", "Downloads", "Pkg", "TOML"]
git-tree-sha1 = "c67b4867f04eba5b202e010fa4cdff817549d69c"
git-tree-sha1 = "aa03729cc19fc581d21b33c7b4a1bab5c96f6345"
repo-rev = "master"
repo-url = "https://github.com/JuliaInterop/Clang.jl.git"
uuid = "40e3b903-d033-50b4-a0cc-940c62c95e31"
Expand Down Expand Up @@ -48,25 +48,25 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"

[[Hwloc_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "ca0f6bf568b4bfc807e7537f081c81e35ceca114"
git-tree-sha1 = "5e19e1e4fa3e71b774ce746274364aef0234634e"
uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
version = "2.10.0+0"
version = "2.11.1+0"

[[InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[JLLWrappers]]
deps = ["Artifacts", "Preferences"]
git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca"
git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
version = "1.5.0"
version = "1.6.0"

[[LAMMPS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "TOML"]
git-tree-sha1 = "f3437b3282fa653f1abb9632cdeca53013194bc8"
git-tree-sha1 = "088be028d89853390a3f4eaf36d459a78ac843e5"
uuid = "5b3ab26d-9607-527c-88ea-8fe5ba57cafe"
version = "2.5.0+0"
version = "2.6.0+0"

[[LazyArtifacts]]
deps = ["Artifacts", "Pkg"]
Expand Down Expand Up @@ -104,9 +104,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[MPICH_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
git-tree-sha1 = "4099bb6809ac109bfc17d521dad33763bcf026b7"
git-tree-sha1 = "19d4bd098928a3263693991500d05d74dbdc2004"
uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
version = "4.2.1+1"
version = "4.2.2+0"

[[MPIPreferences]]
deps = ["Libdl", "Preferences"]
Expand Down Expand Up @@ -145,9 +145,9 @@ version = "1.2.0"

[[OpenMPI_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
git-tree-sha1 = "a9de2f1fc98b92f8856c640bf4aec1ac9b2a0d86"
git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f"
uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
version = "5.0.3+0"
version = "5.0.5+0"

[[Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
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11 changes: 11 additions & 0 deletions src/LAMMPS.jl
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Expand Up @@ -90,6 +90,17 @@ function __init__()
error("The size of the LAMMPS integer type TAGINT has changed! To fix this, you need to manually invalidate the LAMMPS.jl cache.")
IMAGEINT != (API.lammps_extract_setting(C_NULL, "tagint") == 4 ? Int32 : Int64) &&
error("The size of the LAMMPS integer type IMAGEINT has changed! To fix this, you need to manually invalidate the LAMMPS.jl cache.")

if API.lammps_config_has_mpi_support() == 0
@warn "The currently loaded LAMMPS installation does not have MPI enabled! \n" *
"Please provide your own LAMMPS installation with `LAMMPS.set_library()` if you \n" *
"want to run LAMMPS in parallel using MPI."
end

if API.lammps_config_has_exceptions() == 0
@warn "The currently loaded LAMMPS installation doesn't have exceptions enabled! \n" *
"This causes the REPL to crash whenever LAMMPS encounters an error."
end
end


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65 changes: 47 additions & 18 deletions src/api.jl
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Expand Up @@ -143,6 +143,18 @@ function lammps_extract_global(handle, name)
ccall((:lammps_extract_global, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}), handle, name)
end

function lammps_extract_pair_dimension(handle, name)
ccall((:lammps_extract_pair_dimension, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}), handle, name)
end

function lammps_extract_pair(handle, name)
ccall((:lammps_extract_pair, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}), handle, name)
end

function lammps_map_atom(handle, id)
ccall((:lammps_map_atom, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cvoid}), handle, id)
end

function lammps_extract_atom_datatype(handle, name)
ccall((:lammps_extract_atom_datatype, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}), handle, name)
end
Expand All @@ -151,24 +163,36 @@ function lammps_extract_atom(handle, name)
ccall((:lammps_extract_atom, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}), handle, name)
end

function lammps_extract_compute(handle, arg2, arg3, arg4)
ccall((:lammps_extract_compute, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}, Cint, Cint), handle, arg2, arg3, arg4)
function lammps_extract_compute(handle, id, style, type)
ccall((:lammps_extract_compute, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}, Cint, Cint), handle, id, style, type)
end

function lammps_extract_fix(handle, arg2, arg3, arg4, arg5, arg6)
ccall((:lammps_extract_fix, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}, Cint, Cint, Cint, Cint), handle, arg2, arg3, arg4, arg5, arg6)
function lammps_extract_fix(handle, id, style, type, nrow, ncol)
ccall((:lammps_extract_fix, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}, Cint, Cint, Cint, Cint), handle, id, style, type, nrow, ncol)
end

function lammps_extract_variable(handle, arg2, arg3)
ccall((:lammps_extract_variable, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}, Ptr{Cchar}), handle, arg2, arg3)
function lammps_extract_variable(handle, name, group)
ccall((:lammps_extract_variable, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}, Ptr{Cchar}), handle, name, group)
end

function lammps_extract_variable_datatype(handle, name)
ccall((:lammps_extract_variable_datatype, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}), handle, name)
end

function lammps_set_variable(arg1, arg2, arg3)
ccall((:lammps_set_variable, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}, Ptr{Cchar}), arg1, arg2, arg3)
function lammps_set_variable(handle, name, str)
ccall((:lammps_set_variable, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}, Ptr{Cchar}), handle, name, str)
end

function lammps_set_string_variable(handle, name, str)
ccall((:lammps_set_string_variable, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}, Ptr{Cchar}), handle, name, str)
end

function lammps_set_internal_variable(handle, name, value)
ccall((:lammps_set_internal_variable, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}, Cdouble), handle, name, value)
end

function lammps_variable_info(handle, idx, buf, bufsize)
ccall((:lammps_variable_info, liblammps), Cint, (Ptr{Cvoid}, Cint, Ptr{Cchar}, Cint), handle, idx, buf, bufsize)
end

function lammps_gather_atoms(handle, name, type, count, data)
Expand Down Expand Up @@ -259,32 +283,37 @@ function lammps_get_os_info(buffer, buf_size)
ccall((:lammps_get_os_info, liblammps), Cvoid, (Ptr{Cchar}, Cint), buffer, buf_size)
end

# no prototype is found for this function at library.h:233:5, please use with caution
# no prototype is found for this function at library.h:241:5, please use with caution
function lammps_config_has_mpi_support()
ccall((:lammps_config_has_mpi_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:234:5, please use with caution
# no prototype is found for this function at library.h:242:5, please use with caution
function lammps_config_has_gzip_support()
ccall((:lammps_config_has_gzip_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:235:5, please use with caution
# no prototype is found for this function at library.h:243:5, please use with caution
function lammps_config_has_png_support()
ccall((:lammps_config_has_png_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:236:5, please use with caution
# no prototype is found for this function at library.h:244:5, please use with caution
function lammps_config_has_jpeg_support()
ccall((:lammps_config_has_jpeg_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:237:5, please use with caution
# no prototype is found for this function at library.h:245:5, please use with caution
function lammps_config_has_ffmpeg_support()
ccall((:lammps_config_has_ffmpeg_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:238:5, please use with caution
# no prototype is found for this function at library.h:246:5, please use with caution
function lammps_config_has_curl_support()
ccall((:lammps_config_has_curl_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:247:5, please use with caution
function lammps_config_has_exceptions()
ccall((:lammps_config_has_exceptions, liblammps), Cint, ())
end
Expand All @@ -293,7 +322,7 @@ function lammps_config_has_package(arg1)
ccall((:lammps_config_has_package, liblammps), Cint, (Ptr{Cchar},), arg1)
end

# no prototype is found for this function at library.h:241:5, please use with caution
# no prototype is found for this function at library.h:250:5, please use with caution
function lammps_config_package_count()
ccall((:lammps_config_package_count, liblammps), Cint, ())
end
Expand All @@ -306,7 +335,7 @@ function lammps_config_accelerator(arg1, arg2, arg3)
ccall((:lammps_config_accelerator, liblammps), Cint, (Ptr{Cchar}, Ptr{Cchar}, Ptr{Cchar}), arg1, arg2, arg3)
end

# no prototype is found for this function at library.h:245:5, please use with caution
# no prototype is found for this function at library.h:254:5, please use with caution
function lammps_has_gpu_device()
ccall((:lammps_has_gpu_device, liblammps), Cint, ())
end
Expand Down Expand Up @@ -339,7 +368,7 @@ function lammps_id_name(arg1, arg2, arg3, arg4, arg5)
ccall((:lammps_id_name, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}, Cint, Ptr{Cchar}, Cint), arg1, arg2, arg3, arg4, arg5)
end

# no prototype is found for this function at library.h:256:5, please use with caution
# no prototype is found for this function at library.h:265:5, please use with caution
function lammps_plugin_count()
ccall((:lammps_plugin_count, liblammps), Cint, ())
end
Expand Down Expand Up @@ -415,7 +444,7 @@ function lammps_get_last_error_message(handle, buffer, buf_size)
ccall((:lammps_get_last_error_message, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}, Cint), handle, buffer, buf_size)
end

# no prototype is found for this function at library.h:299:5, please use with caution
# no prototype is found for this function at library.h:308:5, please use with caution
function lammps_python_api_version()
ccall((:lammps_python_api_version, liblammps), Cint, ())
end
Expand Down
5 changes: 4 additions & 1 deletion test/runtests.jl
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Expand Up @@ -351,4 +351,7 @@ end
end
end

@test success(pipeline(`$(MPI.mpiexec()) -n 2 $(Base.julia_cmd()) mpitest.jl`, stderr=stderr, stdout=stdout))
@testset "MPI" begin
@test LAMMPS.API.lammps_config_has_mpi_support() != 0
@test success(pipeline(`$(MPI.mpiexec()) -n 2 $(Base.julia_cmd()) mpitest.jl`, stderr=stderr, stdout=stdout))
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Sorry, I meant, make the mpitest.jl fail if it is run without MPI support. In my earlier hybris, I trusted this test to not work without MPI support, but it would just happily run with LAMMPS not using MPI.

end
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