v3.0.0b0 #78
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v3.0.0b0 #78
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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Hi! This is the friendly automated conda-forge-linting service. I wanted to let you know that I linted all conda-recipes in your PR ( Here's what I've got... For recipe:
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@conda-forge-admin, please rerender |
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@conda-forge-admin, please rerender |
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Hi! This is the friendly automated conda-forge-linting service. I just wanted to let you know that I linted all conda-recipes in your PR ( |
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Hi! This is the friendly automated conda-forge-webservice. I tried to rerender for you but ran into some issues. Please check the output logs of the latest webservices GitHub actions workflow run for errors. You can also ping conda-forge/core for further assistance or you can try rerendeing locally. This message was generated by GitHub actions workflow run https://github.com/conda-forge/deepmd-kit-feedstock/actions/runs/9783853775. |
…nda-forge-pinning 2024.07.03.17.45.27
njzjz
commented
Jul 3, 2024
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The second one is a segfault with openmpi + absl:
2024-07-03T20:00:29.2814841Z + export OMPI_MCA_plm=isolated OMPI_MCA_btl_vader_single_copy_mechanism=none OMPI_MCA_rmaps_base_oversubscribe=yes OMPI_MCA_plm_ssh_agent=false
2024-07-03T20:00:29.2815656Z + OMPI_MCA_plm=isolated
2024-07-03T20:00:29.2815930Z + OMPI_MCA_btl_vader_single_copy_mechanism=none
2024-07-03T20:00:29.2816146Z + OMPI_MCA_rmaps_base_oversubscribe=yes
2024-07-03T20:00:29.2816458Z + OMPI_MCA_plm_ssh_agent=false
2024-07-03T20:00:29.2816990Z + mpiexec -n 1 lmp_mpi -in in.lammps
2024-07-03T20:00:29.4367999Z [1f1c0d740e3f:04385] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)
2024-07-03T20:00:29.4559532Z LAMMPS (2 Aug 2023)
2024-07-03T20:00:29.4568122Z OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
2024-07-03T20:00:29.4575016Z using 1 OpenMP thread(s) per MPI task
2024-07-03T20:00:30.0446896Z [1f1c0d740e3f:04385] *** Process received signal ***
2024-07-03T20:00:30.0448123Z [1f1c0d740e3f:04385] Signal: Segmentation fault (11)
2024-07-03T20:00:30.0453336Z [1f1c0d740e3f:04385] Signal code: Address not mapped (1)
2024-07-03T20:00:30.0454407Z [1f1c0d740e3f:04385] Failing at address: 0x8
2024-07-03T20:00:30.0459737Z [1f1c0d740e3f:04385] [ 0] /lib64/libc.so.6(+0x36400)[0x7f43ab885400]
2024-07-03T20:00:30.0462368Z [1f1c0d740e3f:04385] [ 1] /home/conda/feedstock_root/build_artifacts/deepmd-kit_1720035897476/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/../lib/./python3.9/site-packages/tensorflow/../../../libabsl_flags_reflection.so.2401.0.0(_ZN4absl12lts_2024011614flags_internal12FlagRegistry12RegisterFlagERNS0_15CommandLineFlagEPKc+0x99)[0x7f43a1318e09]
2024-07-03T20:00:30.0464226Z [1f1c0d740e3f:04385] [ 2] /home/conda/feedstock_root/build_artifacts/deepmd-kit_1720035897476/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/../lib/./python3.9/site-packages/tensorflow/../../../libabsl_flags_reflection.so.2401.0.0(_ZN4absl12lts_2024011614flags_internal23RegisterCommandLineFlagERNS0_15CommandLineFlagEPKc+0x21)[0x7f43a131a5c1]
2024-07-03T20:00:30.0465530Z [1f1c0d740e3f:04385] [ 3] /home/conda/feedstock_root/build_artifacts/deepmd-kit_1720035897476/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/../lib/./python3.9/site-packages/tensorflow/../../../libabsl_log_flags.so.2401.0.0(+0x3079)[0x7f43a1338079]
2024-07-03T20:00:30.0466184Z [1f1c0d740e3f:04385] [ 4] /lib64/ld-linux-x86-64.so.2(+0xf9c3)[0x7f43b13a99c3]
2024-07-03T20:00:30.0466604Z [1f1c0d740e3f:04385] [ 5] /lib64/ld-linux-x86-64.so.2(+0x1459e)[0x7f43b13ae59e]
2024-07-03T20:00:30.0467010Z [1f1c0d740e3f:04385] [ 6] /lib64/ld-linux-x86-64.so.2(+0xf7d4)[0x7f43b13a97d4]
2024-07-03T20:00:30.0467376Z [1f1c0d740e3f:04385] [ 7] /lib64/ld-linux-x86-64.so.2(+0x13b8b)[0x7f43b13adb8b]
2024-07-03T20:00:30.0467893Z [1f1c0d740e3f:04385] [ 8] /lib64/libdl.so.2(+0xfab)[0x7f43a99fcfab]
2024-07-03T20:00:30.0468252Z [1f1c0d740e3f:04385] [ 9] /lib64/ld-linux-x86-64.so.2(+0xf7d4)[0x7f43b13a97d4]
2024-07-03T20:00:30.0468559Z [1f1c0d740e3f:04385] [10] /lib64/libdl.so.2(+0x15ad)[0x7f43a99fd5ad]
2024-07-03T20:00:30.0468815Z [1f1c0d740e3f:04385] [11] /lib64/libdl.so.2(dlopen+0x31)[0x7f43a99fd041]
2024-07-03T20:00:30.0469716Z [1f1c0d740e3f:04385] [12] /home/conda/feedstock_root/build_artifacts/deepmd-kit_1720035897476/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/../lib/liblammps.so.0(_ZN9LAMMPS_NS11plugin_loadEPKcPNS_6LAMMPSE+0xa6)[0x7f43acd40df6]
2024-07-03T20:00:30.0470980Z [1f1c0d740e3f:04385] [13] /home/conda/feedstock_root/build_artifacts/deepmd-kit_1720035897476/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/../lib/liblammps.so.0(_ZN9LAMMPS_NS16plugin_auto_loadEPNS_6LAMMPSE+0x1a6)[0x7f43acd41446]
2024-07-03T20:00:30.0472135Z [1f1c0d740e3f:04385] [14] /home/conda/feedstock_root/build_artifacts/deepmd-kit_1720035897476/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/../lib/liblammps.so.0(_ZN9LAMMPS_NS6LAMMPSC2EiPPcP19ompi_communicator_t+0xefd)[0x7f43ac5fedfd]
2024-07-03T20:00:30.0472657Z [1f1c0d740e3f:04385] [15] lmp_mpi(+0x2217)[0x556b1653b217]
2024-07-03T20:00:30.0472911Z [1f1c0d740e3f:04385] [16] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f43ab871555]
2024-07-03T20:00:30.0473171Z [1f1c0d740e3f:04385] [17] lmp_mpi(+0x2298)[0x556b1653b298]
2024-07-03T20:00:30.0473388Z [1f1c0d740e3f:04385] *** End of error message ***
2024-07-03T20:00:30.3112890Z --------------------------------------------------------------------------
2024-07-03T20:00:30.3113960Z Primary job terminated normally, but 1 process returned
2024-07-03T20:00:30.3114930Z a non-zero exit code. Per user-direction, the job has been aborted.
2024-07-03T20:00:30.3115645Z --------------------------------------------------------------------------
2024-07-03T20:00:32.5233816Z --------------------------------------------------------------------------
2024-07-03T20:00:32.5235155Z mpiexec noticed that process rank 0 with PID 0 on node 1f1c0d740e3f exited on signal 11 (Segmentation fault).
2024-07-03T20:00:32.5235753Z --------------------------------------------------------------------------
2024-07-03T20:00:33.7626910Z WARNING: Tests failed for deepmd-kit-3.0.0b0-cpu_py39hfac8ecd_mpi_openmpi_0.conda - moving package to /home/conda/feedstock_root/build_artifacts/broken
2024-07-03T20:00:33.8070705Z TESTS FAILED: deepmd-kit-3.0.0b0-cpu_py39hfac8ecd_mpi_openmpi_0.conda
Unclear how to fix it or just skip the test.
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It seems to me that mpich also has the segfault.
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Reproduced on the local machine.
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(gdb) where
#0 0x0000155541a60e09 in absl::lts_20240116::flags_internal::FlagRegistry::RegisterFlag(absl::lts_20240116::CommandLineFlag&, char const*) ()
from /home/jz748/anaconda3/envs/test-deepmd-build/bin/../lib/./python3.11/site-packages/tensorflow/../../../libabsl_flags_reflection.so.2401.0.0
#1 0x0000155541a625c1 in absl::lts_20240116::flags_internal::RegisterCommandLineFlag(absl::lts_20240116::CommandLineFlag&, char const*) ()
from /home/jz748/anaconda3/envs/test-deepmd-build/bin/../lib/./python3.11/site-packages/tensorflow/../../../libabsl_flags_reflection.so.2401.0.0
#2 0x0000155541a80079 in _GLOBAL__sub_I_flags.cc ()
from /home/jz748/anaconda3/envs/test-deepmd-build/bin/../lib/./python3.11/site-packages/tensorflow/../../../libabsl_log_flags.so.2401.0.0
#3 0x0000155555525237 in call_init (env=0x55555567dbf0, argv=0x7fffffffad58, argc=3, l=<optimized out>) at dl-init.c:74
#4 call_init (l=<optimized out>, argc=3, argv=0x7fffffffad58, env=0x55555567dbf0) at dl-init.c:26
#5 0x000015555552532d in _dl_init (main_map=0x555555780eb0, argc=3, argv=0x7fffffffad58, env=0x55555567dbf0) at dl-init.c:121
#6 0x00001555555215c2 in __GI__dl_catch_exception (exception=exception@entry=0x0, operate=operate@entry=0x15555552bf50 <call_dl_init>,
args=args@entry=0x7fffffffa290) at dl-catch.c:211
#7 0x000015555552beec in dl_open_worker (a=a@entry=0x7fffffffa440) at dl-open.c:827
#8 0x0000155555521523 in __GI__dl_catch_exception (exception=exception@entry=0x7fffffffa420,
operate=operate@entry=0x15555552be50 <dl_open_worker>, args=args@entry=0x7fffffffa440) at dl-catch.c:237
#9 0x000015555552c2e4 in _dl_open (file=0x555555780cc0 "/home/jz748/anaconda3/envs/test-deepmd-build/lib/deepmd_lmp/dpplugin.so",
mode=<optimized out>, caller_dlopen=0x155550f40916 <LAMMPS_NS::plugin_load(char const*, LAMMPS_NS::LAMMPS*)+166>, nsid=<optimized out>,
argc=3, argv=0x7fffffffad58, env=0x55555567dbf0) at dl-open.c:903
#10 0x000015554fcc7714 in dlopen_doit () from /lib64/libc.so.6
#11 0x0000155555521523 in __GI__dl_catch_exception (exception=exception@entry=0x7fffffffa630, operate=0x15554fcc76b0 <dlopen_doit>,
args=0x7fffffffa6f0) at dl-catch.c:237
#12 0x0000155555521679 in _dl_catch_error (objname=0x7fffffffa698, errstring=0x7fffffffa6a0, mallocedp=0x7fffffffa697, operate=<optimized out>,
args=<optimized out>) at dl-catch.c:256
#13 0x000015554fcc71f3 in _dlerror_run () from /lib64/libc.so.6
#14 0x000015554fcc77cf in dlopen@GLIBC_2.2.5 () from /lib64/libc.so.6
#15 0x0000155550f40916 in LAMMPS_NS::plugin_load(char const*, LAMMPS_NS::LAMMPS*) ()
from /home/jz748/anaconda3/envs/test-deepmd-build/bin/../lib/liblammps.so.0
#16 0x0000155550f40f66 in LAMMPS_NS::plugin_auto_load(LAMMPS_NS::LAMMPS*) ()
from /home/jz748/anaconda3/envs/test-deepmd-build/bin/../lib/liblammps.so.0
#17 0x00001555507fe6ed in LAMMPS_NS::LAMMPS::LAMMPS(int, char**, ompi_communicator_t*) ()
from /home/jz748/anaconda3/envs/test-deepmd-build/bin/../lib/liblammps.so.0
#18 0x0000555555556217 in main ()
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As a workaround, I pinned tensorflow to 2.15 and pytorch to 2.1, and submitted conda-forge/abseil-cpp-feedstock#79.
…repodata-patches-feedstock#787 Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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@conda-forge-admin please rerender |
…nda-forge-pinning 2024.07.04.09.14.11
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@conda-forge-admin please rerender |
…nda-forge-pinning 2024.07.04.09.14.11
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@conda-forge-admin please rerender |
…nda-forge-pinning 2024.07.04.09.14.11
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0(if the version changed)conda-smithy(Use the phrase@conda-forge-admin, please rerenderin a comment in this PR for automated rerendering)