ModuleNotFoundError: No module named 'mpi4py'
George Miloshevich
I managed to install Dedalus on Virtualbox Ubuntu 16.04 before, I don't remember what I did then. This time I installed Dedalus on newly installed Ubuntu 16.04 and when I tried to compile the first Tutorial in jupyter notebook I got:
ModuleNotFoundError Traceback (most recent call last) <ipython-input-1-5250cb4fc73f> in <module>() ----> 1 from dedalus import public as de 2 import numpy as np 3 import matplotlib.pyplot as plt 4 5 de.logging_setup.rootlogger.setLevel('ERROR') ~/dedalus/src/dedalus/dedalus/public.py in <module>() 5 6 # Import custom logging to setup rootlogger ----> 7 from .tools import logging as logging_setup 8 9 from .core import future as _future ~/dedalus/src/dedalus/dedalus/tools/logging.py in <module>() 6 import pathlib 7 import logging ----> 8 from mpi4py im 9 import os 10 import sys ModuleNotFoundError: No module named 'mpi4py'
Perhaps it is noteworthy to mention that after installing Dedalus I installed Anaconda3 to have jupyter notebook. Perhaps I need to manually provide paths but I don't know how to do this. I tried running install.sh again but still the same problem persists.
thanks,
George
George Miloshevich
I was pressing enter when Dedalus installer.sh prompts for enter before installing all the necessary packages.
The correct order that works for me is to first do:
sudo apt-get install libatlas-base-dev libatlas3-base libopenmpi-dev openmpi-bin libssl-dev build-essential libncurses5 libncurses5-dev zip uuid-dev libfreetype6-dev tk-dev libhdf5-dev mercurial libsqlite3-dev gfortran
and then bash isntall.sh
Afterwards jupyter notebook can be installed via
pip3 install --upgrade pip
pip3 install jupyter
avi....@gmail.com
In [1]: from dedalus import public as de
[ThinkPad-X220-Tablet:14899] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv.so: undefined symbol: opal_show_help (ignored)
[ThinkPad-X220-Tablet:14899] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap.so: undefined symbol: opal_show_help (ignored)
[ThinkPad-X220-Tablet:14899] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: /usr/lib/openmpi/lib/openmpi/mca_shmem_posix.so: undefined symbol: opal_shmem_base_framework (ignored)
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
opal_shmem_base_select failed
--> Returned value -1 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
opal_init failed
--> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: ompi_rte_init failed
--> Returned "Error" (-1) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init_thread
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[ThinkPad-X220-Tablet:14899] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
My computer is:
Linux ThinkPad-X220-Tablet 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
A Ranjan
If I give the same command from python3 shell, I get a different error
>>> from dedalus import public as de
*** Error in `python3': free(): invalid pointer: 0x00007f62632ae828 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f626251d7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f626252637a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f626252a53c]
python3(PyOS_Readline+0xec)[0x5c60cc]
python3[0x447f90]
python3[0x449a48]
python3(PyTokenizer_Get+0x9)[0x44a919]
python3[0x44643e]
python3(PyParser_ASTFromFileObject+0xa3)[0x428a23]
python3(PyRun_InteractiveOneObject+0x122)[0x428c62]
python3(PyRun_InteractiveLoopFlags+0x6e)[0x428fee]
python3(PyRun_AnyFileExFlags+0x3c)[0x42911c]
python3(Py_Main+0xe4f)[0x43bcef]
python3(main+0x162)[0x41dd72]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f62624c6830]
python3(_start+0x29)[0x41de49]
======= Memory map: ========
00400000-00666000 r-xp 00000000 08:15 536600 /home/avishek/dedalus/bin/python3.6
00865000-00866000 r--p 00265000 08:15 536600 /home/avishek/dedalus/bin/python3.6
00866000-008ca000 rw-p 00266000 08:15 536600 /home/avishek/dedalus/bin/python3.6
008ca000-008fb000 rw-p 00000000 00:00 0
00f5a000-01036000 rw-p 00000000 00:00 0 [heap]
7f625c000000-7f625c021000 rw-p 00000000 00:00 0
7f625c021000-7f6260000000 ---p 00000000 00:00 0
7f6261883000-7f6261899000 r-xp 00000000 08:15 1447160 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6261899000-7f6261a98000 ---p 00016000 08:15 1447160 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6261a98000-7f6261a99000 rw-p 00015000 08:15 1447160 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6261a99000-7f6261abe000 r-xp 00000000 08:15 1447294 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f6261abe000-7f6261cbd000 ---p 00025000 08:15 1447294 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f6261cbd000-7f6261cc1000 r--p 00024000 08:15 1447294 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f6261cc1000-7f6261cc2000 rw-p 00028000 08:15 1447294 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f6261cc2000-7f6261cff000 r-xp 00000000 08:15 939554 /home/avishek/dedalus/lib/python3.6/site-packages/readline.cpython-36m-x86_64-linux-gnu.so
7f6261cff000-7f6261efe000 ---p 0003d000 08:15 939554 /home/avishek/dedalus/lib/python3.6/site-packages/readline.cpython-36m-x86_64-linux-gnu.so
7f6261efe000-7f6261f00000 r--p 0003c000 08:15 939554 /home/avishek/dedalus/lib/python3.6/site-packages/readline.cpython-36m-x86_64-linux-gnu.so
7f6261f00000-7f6261f07000 rw-p 0003e000 08:15 939554 /home/avishek/dedalus/lib/python3.6/site-packages/readline.cpython-36m-x86_64-linux-gnu.so
7f6261f07000-7f6261f49000 rw-p 00000000 00:00 0
7f6261f49000-7f6261f4b000 r-xp 00000000 08:15 537531 /home/avishek/dedalus/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
7f6261f4b000-7f626214b000 ---p 00002000 08:15 537531 /home/avishek/dedalus/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
7f626214b000-7f626214c000 r--p 00002000 08:15 537531 /home/avishek/dedalus/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
7f626214c000-7f626214e000 rw-p 00003000 08:15 537531 /home/avishek/dedalus/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
7f626214e000-7f62621ce000 rw-p 00000000 00:00 0
7f62621ce000-7f62624a6000 r--p 00000000 08:15 1835405 /usr/lib/locale/locale-archive
7f62624a6000-7f6262666000 r-xp 00000000 08:15 1441876 /lib/x86_64-linux-gnu/libc-2.23.so
7f6262666000-7f6262866000 ---p 001c0000 08:15 1441876 /lib/x86_64-linux-gnu/libc-2.23.so
7f6262866000-7f626286a000 r--p 001c0000 08:15 1441876 /lib/x86_64-linux-gnu/libc-2.23.so
7f626286a000-7f626286c000 rw-p 001c4000 08:15 1441876 /lib/x86_64-linux-gnu/libc-2.23.so
7f626286c000-7f6262870000 rw-p 00000000 00:00 0
7f6262870000-7f6262978000 r-xp 00000000 08:15 1441798 /lib/x86_64-linux-gnu/libm-2.23.so
7f6262978000-7f6262b77000 ---p 00108000 08:15 1441798 /lib/x86_64-linux-gnu/libm-2.23.so
7f6262b77000-7f6262b78000 r--p 00107000 08:15 1441798 /lib/x86_64-linux-gnu/libm-2.23.so
7f6262b78000-7f6262b79000 rw-p 00108000 08:15 1441798 /lib/x86_64-linux-gnu/libm-2.23.so
7f6262b79000-7f6262b7b000 r-xp 00000000 08:15 1441883 /lib/x86_64-linux-gnu/libutil-2.23.so
7f6262b7b000-7f6262d7a000 ---p 00002000 08:15 1441883 /lib/x86_64-linux-gnu/libutil-2.23.so
7f6262d7a000-7f6262d7b000 r--p 00001000 08:15 1441883 /lib/x86_64-linux-gnu/libutil-2.23.so
7f6262d7b000-7f6262d7c000 rw-p 00002000 08:15 1441883 /lib/x86_64-linux-gnu/libutil-2.23.so
7f6262d7c000-7f6262d7f000 r-xp 00000000 08:15 1441878 /lib/x86_64-linux-gnu/libdl-2.23.so
7f6262d7f000-7f6262f7e000 ---p 00003000 08:15 1441878 /lib/x86_64-linux-gnu/libdl-2.23.so
7f6262f7e000-7f6262f7f000 r--p 00002000 08:15 1441878 /lib/x86_64-linux-gnu/libdl-2.23.so
7f6262f7f000-7f6262f80000 rw-p 00003000 08:15 1441878 /lib/x86_64-linux-gnu/libdl-2.23.so
7f6262f80000-7f6262f98000 r-xp 00000000 08:15 1441818 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6262f98000-7f6263197000 ---p 00018000 08:15 1441818 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6263197000-7f6263198000 r--p 00017000 08:15 1441818 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6263198000-7f6263199000 rw-p 00018000 08:15 1441818 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6263199000-7f626319d000 rw-p 00000000 00:00 0
7f626319d000-7f62631c3000 r-xp 00000000 08:15 1441810 /lib/x86_64-linux-gnu/ld-2.23.so
7f62631fd000-7f62633a7000 rw-p 00000000 00:00 0
7f62633ba000-7f62633bb000 rw-p 00000000 00:00 0
7f62633bb000-7f62633c2000 r--s 00000000 08:15 1129 /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f62633c2000-7f62633c3000 r--p 00025000 08:15 1441810 /lib/x86_64-linux-gnu/ld-2.23.so
7f62633c3000-7f62633c4000 rw-p 00026000 08:15 1441810 /lib/x86_64-linux-gnu/ld-2.23.so
7f62633c4000-7f62633c5000 rw-p 00000000 00:00 0
7ffe7f7f7000-7ffe7f818000 rw-p 00000000 00:00 0 [stack]
7ffe7f931000-7ffe7f933000 r--p 00000000 00:00 0 [vvar]
7ffe7f933000-7ffe7f935000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
(dedalus)avishek@ThinkPad-X220-Tablet:~/dedalus/src/dedalus$