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Fix analysis imports #726

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Fix analysis imports #726

wants to merge 5 commits into from

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AlexanderSinn
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@AlexanderSinn AlexanderSinn commented Mar 26, 2022 •
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based on #724 and #725

On Maxwell (DESY) this crashes:

import matplotlib # or scipy
import openpmd_viewer

but this works:

import openpmd_viewer
import matplotlib
import scipy

This PR changes the import order in all analysis python scripts to run on Maxwell (after the dependencies are updated with pip).

Crash message:

[asinn@max-mpag001]~% module load maxwell gcc/9.3 openmpi/4 hdf5/1.10.6
[asinn@max-mpag001]~% python3
Python 3.6.8 (default, Nov 16 2020, 16:55:22)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-44)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> import openpmd_viewer
*** Error in `python3': free(): invalid pointer: 0x00002b1ef9237c20 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2b1ce4da1329]
/usr/lib64/llvm4.0/lib/libLLVM-4.0.so(_ZNSt6locale5_Impl16_M_install_facetEPKNS_2idEPKNS_5facetE+0x142)[0x2b1ef81ddd42]
/usr/lib64/llvm4.0/lib/libLLVM-4.0.so(_ZNSt6locale5_ImplC2Em+0x1e3)[0x2b1ef81c1873]
/usr/lib64/llvm4.0/lib/libLLVM-4.0.so(_ZNSt6locale18_S_initialize_onceEv+0x15)[0x2b1ef81c27e5]
/lib64/libpthread.so.0(+0x620b)[0x2b1ce440120b]
/usr/lib64/llvm4.0/lib/libLLVM-4.0.so(_ZNSt6locale13_S_initializeEv+0x21)[0x2b1ef81c2831]
/usr/lib64/llvm4.0/lib/libLLVM-4.0.so(_ZNSt6localeC1Ev+0x13)[0x2b1ef81c2873]
/usr/lib64/python3.6/site-packages/llvmlite/binding/libllvmlite.so(LLVMPY_GetHostCPUFeatures+0x75)[0x2b1ef6356cd5]
/lib64/libffi.so.6(ffi_call_unix64+0x4c)[0x2b1ef35ede2c]
/lib64/libffi.so.6(ffi_call+0x1f5)[0x2b1ef35ed755]
/usr/lib64/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so(_ctypes_callproc+0x2a0)[0x2b1ef33d8680]
/usr/lib64/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so(+0x97c6)[0x2b1ef33d17c6]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x90)[0x2b1ce3f7bd20]
/lib64/libpython3.6m.so.1.0(+0x1522fc)[0x2b1ce40252fc]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(+0x151f3a)[0x2b1ce4024f3a]
/lib64/libpython3.6m.so.1.0(+0x152273)[0x2b1ce4025273]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(+0x151f3a)[0x2b1ce4024f3a]
/lib64/libpython3.6m.so.1.0(+0x152273)[0x2b1ce4025273]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(+0x151f3a)[0x2b1ce4024f3a]
/lib64/libpython3.6m.so.1.0(+0x152273)[0x2b1ce4025273]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(+0x151f3a)[0x2b1ce4024f3a]
/lib64/libpython3.6m.so.1.0(+0x152273)[0x2b1ce4025273]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(+0x151f3a)[0x2b1ce4024f3a]
/lib64/libpython3.6m.so.1.0(+0x152273)[0x2b1ce4025273]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x15a)[0x2b1ce402626a]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x10e)[0x2b1ce3f7bd9e]
/lib64/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0x61)[0x2b1ce3f7beb1]
/lib64/libpython3.6m.so.1.0(PyObject_Call+0x43)[0x2b1ce3f7bb23]
/lib64/libpython3.6m.so.1.0(+0xfbc75)[0x2b1ce3fcec75]
/lib64/libpython3.6m.so.1.0(+0xf8632)[0x2b1ce3fcb632]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x90)[0x2b1ce3f7bd20]
/lib64/libpython3.6m.so.1.0(+0x1522fc)[0x2b1ce40252fc]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(+0x151f3a)[0x2b1ce4024f3a]
/lib64/libpython3.6m.so.1.0(+0x152273)[0x2b1ce4025273]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x15a)[0x2b1ce402626a]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x10e)[0x2b1ce3f7bd9e]
/lib64/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0x61)[0x2b1ce3f7beb1]
/lib64/libpython3.6m.so.1.0(PyObject_Call+0x43)[0x2b1ce3f7bb23]
/lib64/libpython3.6m.so.1.0(+0xfbc75)[0x2b1ce3fcec75]
/lib64/libpython3.6m.so.1.0(+0xf8632)[0x2b1ce3fcb632]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x90)[0x2b1ce3f7bd20]
/lib64/libpython3.6m.so.1.0(+0x1522fc)[0x2b1ce40252fc]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(+0x151f3a)[0x2b1ce4024f3a]
/lib64/libpython3.6m.so.1.0(+0x152273)[0x2b1ce4025273]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x2b1ce4019a17]
/lib64/libpython3.6m.so.1.0(+0x151317)[0x2b1ce4024317]
/lib64/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x24f)[0x2b1ce402635f]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x10e)[0x2b1ce3f7bd9e]
/lib64/libpython3.6m.so.1.0(PyObject_CallFunctionObjArgs+0xe2)[0x2b1ce3f7d232]
/lib64/libpython3.6m.so.1.0(_PyObject_GenericGetAttrWithDict+0x1c1)[0x2b1ce3fbb081]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x439)[0x2b1ce4019aa9]
/lib64/libpython3.6m.so.1.0(PyEval_EvalCodeEx+0x22d)[0x2b1ce40255ed]
/lib64/libpython3.6m.so.1.0(+0xc0c93)[0x2b1ce3f93c93]
/lib64/libpython3.6m.so.1.0(PyObject_Call+0x43)[0x2b1ce3f7bb23]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:08 1057408                            /usr/bin/python3.6
00601000-00602000 r--p 00001000 08:08 1057408                            /usr/bin/python3.6
00602000-00603000 rw-p 00002000 08:08 1057408                            /usr/bin/python3.6
01d4f000-026a5000 rw-p 00000000 00:00 0                                  [heap]
2b1ce3caf000-2b1ce3cd1000 r-xp 00000000 08:08 1049209                    /usr/lib64/ld-2.17.so
2b1ce3cd1000-2b1ce3cd2000 rw-p 00000000 00:00 0
2b1ce3cd2000-2b1ce3cd9000 r--s 00000000 08:08 1314464                    /usr/lib64/gconv/gconv-modules.cache
2b1ce3cd9000-2b1ce3cdc000 r--p 00000000 00:30 1629726                    /software/gcc/9.3.0/lib64/libgcc_s.so.1
2b1ce3cdc000-2b1ce3ced000 r-xp 00003000 00:30 1629726                    /software/gcc/9.3.0/lib64/libgcc_s.so.1
2b1ce3ced000-2b1ce3cf1000 r--p 00014000 00:30 1629726                    /software/gcc/9.3.0/lib64/libgcc_s.so.1
2b1ce3cf1000-2b1ce3cf2000 r--p 00017000 00:30 1629726                    /software/gcc/9.3.0/lib64/libgcc_s.so.1
2b1ce3cf2000-2b1ce3cf3000 rw-p 00018000 00:30 1629726                    /software/gcc/9.3.0/lib64/libgcc_s.so.1
2b1ce3cf3000-2b1ce3cf4000 rwxp 00000000 00:00 0
2b1ce3cf4000-2b1ce3cf5000 rw-p 00000000 00:00 0
2b1ce3cfe000-2b1ce3cff000 rw-p 00000000 00:00 0
2b1ce3d10000-2b1ce3e95000 rw-p 00000000 00:00 0
2b1ce3ed0000-2b1ce3ed1000 r--p 00021000 08:08 1049209                    /usr/lib64/ld-2.17.so
2b1ce3ed1000-2b1ce3ed2000 rw-p 00022000 08:08 1049209                    /usr/lib64/ld-2.17.so
2b1ce3ed2000-2b1ce3ed3000 rw-p 00000000 00:00 0
2b1ce3ed3000-2b1ce4160000 r-xp 00000000 08:08 1057394                    /usr/lib64/libpython3.6m.so.1.0
2b1ce4160000-2b1ce4360000 ---p 0028d000 08:08 1057394                    /usr/lib64/libpython3.6m.so.1.0
2b1ce4360000-2b1ce4363000 r--p 0028d000 08:08 1057394                    /usr/lib64/libpython3.6m.so.1.0
2b1ce4363000-2b1ce43c9000 rw-p 00290000 08:08 1057394                    /usr/lib64/libpython3.6m.so.1.0
2b1ce43c9000-2b1ce43fb000 rw-p 00000000 00:00 0
2b1ce43fb000-2b1ce4412000 r-xp 00000000 08:08 1049246                    /usr/lib64/libpthread-2.17.so
2b1ce4412000-2b1ce4611000 ---p 00017000 08:08 1049246                    /usr/lib64/libpthread-2.17.so
2b1ce4611000-2b1ce4612000 r--p 00016000 08:08 1049246                    /usr/lib64/libpthread-2.17.so
2b1ce4612000-2b1ce4613000 rw-p 00017000 08:08 1049246                    /usr/lib64/libpthread-2.17.so
2b1ce4613000-2b1ce4617000 rw-p 00000000 00:00 0
2b1ce4617000-2b1ce4619000 r-xp 00000000 08:08 1049226                    /usr/lib64/libdl-2.17.so
2b1ce4619000-2b1ce4819000 ---p 00002000 08:08 1049226                    /usr/lib64/libdl-2.17.so
2b1ce4819000-2b1ce481a000 r--p 00002000 08:08 1049226                    /usr/lib64/libdl-2.17.so
2b1ce481a000-2b1ce481b000 rw-p 00003000 08:08 1049226                    /usr/lib64/libdl-2.17.so
2b1ce481b000-2b1ce481d000 r-xp 00000000 08:08 1049254                    /usr/lib64/libutil-2.17.so
2b1ce481d000-2b1ce4a1c000 ---p 00002000 08:08 1049254                    /usr/lib64/libutil-2.17.so
2b1ce4a1c000-2b1ce4a1d000 r--p 00001000 08:08 1049254                    /usr/lib64/libutil-2.17.so
2b1ce4a1d000-2b1ce4a1e000 rw-p 00002000 08:08 1049254                    /usr/lib64/libutil-2.17.so
2b1ce4a1e000-2b1ce4b1f000 r-xp 00000000 08:08 1049228                    /usr/lib64/libm-2.17.so
2b1ce4b1f000-2b1ce4d1e000 ---p 00101000 08:08 1049228                    /usr/lib64/libm-2.17.so
2b1ce4d1e000-2b1ce4d1f000 r--p 00100000 08:08 1049228                    /usr/lib64/libm-2.17.so
2b1ce4d1f000-2b1ce4d20000 rw-p 00101000 08:08 1049228                    /usr/lib64/libm-2.17.so
2b1ce4d20000-2b1ce4ee4000 r-xp 00000000 08:08 1049220                    /usr/lib64/libc-2.17.so
2b1ce4ee4000-2b1ce50e3000 ---p 001c4000 08:08 1049220                    /usr/lib64/libc-2.17.so
2b1ce50e3000-2b1ce50e7000 r--p 001c3000 08:08 1049220                    /usr/lib64/libc-2.17.so
2b1ce50e7000-2b1ce50e9000 rw-p 001c7000 08:08 1049220                    /usr/lib64/libc-2.17.so
2b1ce50e9000-2b1ce50ee000 rw-p 00000000 00:00 0
2b1ce50ee000-2b1ceb631000 r--p 00000000 08:08 1060787                    /usr/lib/locale/locale-archive
2b1ceb631000-2b1ceb637000 r-xp 00000000 08:08 2493237                    /usr/lib64/python3.6/lib-dynload/readline.cpython-36m-x86_64-linux-gnu.so
2b1ceb637000-2b1ceb836000 ---p 00006000 08:08 2493237                    /usr/lib64/python3.6/lib-dynload/readline.cpython-36m-x86_64-linux-gnu.so
2b1ceb836000-2b1ceb837000 r--p 00005000 08:08 2493237                    /usr/lib64/python3.6/lib-dynload/readline.cpython-36m-x86_64-linux-gnu.so
2b1ceb837000-2b1ceb839000 rw-p 00006000 08:08 2493237                    /usr/lib64/python3.6/lib-dynload/readline.cpython-36m-x86_64-linux-gnu.so
2b1ceb839000-2b1ceb9f9000 rw-p 00000000 00:00 0
2b1ceba32000-2b1cebab2000 rw-p 00000000 00:00 0
2b1cebab2000-2b1cebab5000 r-xp 00000000 08:08 2493208                    /usr/lib64/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2b1cebab5000-2b1cebcb4000 ---p 00003000 08:08 2493208                    /usr/lib64/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2b1cebcb4000-2b1cebcb5000 r--p 00002000 08:08 2493208                    /usr/lib64/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2b1cebcb5000-2b1cebcb7000 rw-p 00003000 08:08 2493208                    /usr/lib64/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2b1cebcb7000-2b1cebcf7000 rw-p 00000000 00:00 0
2b1cebcf7000-2b1cebd33000 r-xp 00000000 08:08 1049589                    /usr/lib64/libreadline.so.6.2
2b1cebd33000-2b1cebf33000 ---p 0003c000 08:08 1049589                    /usr/lib64/libreadline.so.6.2
2b1cebf33000-2b1cebf35000 r--p 0003c000 08:08 1049589                    /usr/lib64/libreadline.so.6.2
2b1cebf35000-2b1cebf3b000 rw-p 0003e000 08:08 1049589                    /usr/lib64/libreadline.so.6.2
2b1cebf3b000-2b1cebf3d000 rw-p 00000000 00:00 0
2b1cebf3d000-2b1cebf62000 r-xp 00000000 08:08 1049290                    /usr/lib64/libtinfo.so.5.9
2b1cebf62000-2b1cec162000 ---p 00025000 08:08 1049290                    /usr/lib64/libtinfo.so.5.9
2b1cec162000-2b1cec166000 r--p 00025000 08:08 1049290                    /usr/lib64/libtinfo.so.5.9
2b1cec166000-2b1cec167000 rw-p 00029000 08:08 1049290                    /usr/lib64/libtinfo.so.5.9
2b1cec167000-2b1cec168000 r-xp 00000000 08:08 2493215                    /usr/lib64/python3.6/lib-dynload/_opcode.cpython-36m-x86_64-linux-gnu.so
2b1cec168000-2b1cec367000 ---p 00001000 08:08 2493215                    /usr/lib64/python3.6/lib-dynload/_opcode.cpython-36m-x86_64-linux-gnu.so
2b1cec367000-2b1cec368000 r--p 00000000 08:08 2493215                    /usr/lib64/python3.6/lib-dynload/_opcode.cpython-36m-x86_64-linux-gnu.so
2b1cec368000-2b1cec369000 rw-p 00001000 08:08 2493215                    /usr/lib64/python3.6/lib-dynload/_opcode.cpython-36m-x86_64-linux-gnu.so
2b1cec369000-2b1cec36f000 r-xp 00000000 08:08 2493245                    /usr/lib64/python3.6/lib-dynload/zlib.cpython-36m-x86_64-linux-gnu.so
2b1cec36f000-2b1cec56e000 ---p 00006000 08:08 2493245                    /usr/lib64/python3.6/lib-dynload/zlib.cpython-36m-x86_64-linux-gnu.so
2b1cec56e000-2b1cec56f000 r--p 00005000 08:08 2493245                    /usr/lib64/python3.6/lib-dynload/zlib.cpython-36m-x86_64-linux-gnu.so
2b1cec56f000-2b1cec571000 rw-p 00006000 08:08 2493245                    /usr/lib64/python3.6/lib-dynload/zlib.cpython-36m-x86_64-linux-gnu.so
2b1cec5af000-2b1cec5c4000 r-xp 00000000 08:08 1049410                    /usr/lib64/libz.so.1.2.7
2b1cec5c4000-2b1cec7c3000 ---p 00015000 08:08 1049410                    /usr/lib64/libz.so.1.2.7
2b1cec7c3000-2b1cec7c4000 r--p 00014000 08:08 1049410                    /usr/lib64/libz.so.1.2.7
2b1cec7c4000-2b1cec7c5000 rw-p 00015000 08:08 1049410                    /usr/lib64/libz.so.1.2.7
2b1cec7c5000-2b1cec7c9000 r-xp 00000000 08:08 2493190                    /usr/lib64/python3.6/lib-dynload/_bz2.cpython-36m-x86_64-linux-gnu.so
2b1cec7c9000-2b1cec9c8000 ---p 00004000 08:08 2493190                    /usr/lib64/python3.6/lib-dynload/_bz2.cpython-36m-x86_64-linux-gnu.so
2b1cec9c8000-2b1cec9c9000 r--p 00003000 08:08 2493190                    /usr/lib64/python3.6/lib-dynload/_bz2.cpython-36m-x86_64-linux-gnu.so
2b1cec9c9000-2b1cec9ca000 rw-p 00004000 08:08 2493190                    /usr/lib64/python3.6/lib-dynload/_bz2.cpython-36m-x86_64-linux-gnu.so
2b1cec9ca000-2b1cec9d9000 r-xp 00000000 08:08 1049527                    /usr/lib64/libbz2.so.1.0.6
2b1cec9d9000-2b1cecbd8000 ---p 0000f000 08:08 1049527                    /usr/lib64/libbz2.so.1.0.6
2b1cecbd8000-2b1cecbd9000 r--p 0000e000 08:08 1049527                    /usr/lib64/libbz2.so.1.0.6
2b1cecbd9000-2b1cecbda000 rw-p 0000f000 08:08 1049527                    /usr/lib64/libbz2.so.1.0.6
2b1cecbda000-2b1cecbe1000 r-xp 00000000 08:08 2493212                    /usr/lib64/python3.6/lib-dynload/_lzma.cpython-36m-x86_64-linux-gnu.so
2b1cecbe1000-2b1cecde0000 ---p 00007000 08:08 2493212                    /usr/lib64/python3.6/lib-dynload/_lzma.cpython-36m-x86_64-linux-gnu.so
2b1cecde0000-2b1cecde1000 r--p 00006000 08:08 2493212                    /usr/lib64/python3.6/lib-dynload/_lzma.cpython-36m-x86_64-linux-gnu.so
2b1cecde1000-2b1cecde3000 rw-p 00007000 08:08 2493212                    /usr/lib64/python3.6/lib-dynload/_lzma.cpython-36m-x86_64-linux-gnu.so
2b1cecde3000-2b1cece08000 r-xp 00000000 08:08 1049423                    /usr/lib64/liblzma.so.5.2.2
2b1cece08000-2b1ced007000 ---p 00025000 08:08 1049423                    /usr/lib64/liblzma.so.5.2.2
2b1ced007000-2b1ced008000 r--p 00024000 08:08 1049423                    /usr/lib64/liblzma.so.5.2.2
2b1ced008000-2b1ced009000 rw-p 00025000 08:08 1049423                    /usr/lib64/liblzma.so.5.2.2
2b1ced009000-2b1ced00b000 r-xp 00000000 08:08 2493230                    /usr/lib64/python3.6/lib-dynload/grp.cpython-36m-x86_64-linux-gnu.so
2b1ced00b000-2b1ced20a000 ---p 00002000 08:08 2493230                    /usr/lib64/python3.6/lib-dynload/grp.cpython-36m-x86_64-linux-gnu.so
2b1ced20a000-2b1ced20b000 r--p 00001000 08:08 2493230                    /usr/lib64/python3.6/lib-dynload/grp.cpython-36m-x86_64-linux-gnu.so
2b1ced20b000-2b1ced20c000 rw-p 00002000 08:08 2493230                    /usr/lib64/python3.6/lib-dynload/grp.cpython-36m-x86_64-linux-gnu.so
2b1ced20c000-2b1ced20f000 r-xp 00000000 08:08 2493217                    /usr/lib64/python3.6/lib-dynload/_posixsubprocess.cpython-36m-x86_64-linux-gnu.so
2b1ced20f000-2b1ced40e000 ---p 00003000 08:08 2493217                    /usr/lib64/python3.6/lib-dynload/_posixsubprocess.cpython-36m-x86_64-linux-gnu.so
2b1ced40e000-2b1ced40f000 r--p 00002000 08:08 2493217                    /usr/lib64/python3.6/lib-dynload/_posixsubprocess.cpython-36m-x86_64-linux-gnu.so
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2b1efc000000-2b1efc021000 rw-p 00000000 00:00 0
2b1efc021000-2b1f00000000 ---p 00000000 00:00 0
7ffff9c18000-7ffff9c3a000 rw-p 00000000 00:00 0                          [stack]
7ffff9d91000-7ffff9d93000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
zsh: abort      python3
  • Small enough (< few 100s of lines), otherwise it should probably be split into smaller PRs
  • Tested (describe the tests in the PR description)
  • Runs on GPU (basic: the code compiles and run well with the new module)
  • Contains an automated test (checksum and/or comparison with theory)
  • Documented: all elements (classes and their members, functions, namespaces, etc.) are documented
  • Constified (All that can be const is const)
  • Code is clean (no unwanted comments, )
  • Style and code conventions are respected at the bottom of https://github.com/Hi-PACE/hipace
  • Proper label and GitHub project, if applicable

@AlexanderSinn
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module load python/3.9

also fixes this

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@AlexanderSinn