Incubator-mxnet: libcblas.so.3: cannot open shared object file: No such file or directory

[salemmohammed]

Hi all,

Operating System:
I am working on a cluster of 3 machines AWS ubuntu 14.04 and Python2.7.
I am following the official site for installation and running the code for distributed training.

When I execute this:

../../tools/launch.py -n 2 -H hosts --sync-dst-dir /tmp/mxnet \
python train_mnist.py --network lenet --kv-store dist_sync

This is the error:

Traceback (most recent call last):
File "train_mnist.py", line 10, in
from common import find_mxnet, fit
File "/tmp/mxnet/common/find_mxnet.py", line 4, in
import mxnet as mx
File "/tmp/mxnet/mxnet/__init__.py", line 7, in
from .base import MXNetError
File "/tmp/mxnet/mxnet/base.py", line 46, in
_LIB = _load_lib()
File "/tmp/mxnet/mxnet/base.py", line 38, in _load_lib
lib = ctypes.CDLL(lib_path[0], ctypes.RTLD_GLOBAL)
File "/usr/lib/python2.7/ctypes/__init__.py", line 365, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libcblas.so.3: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "train_mnist.py", line 10, in
from common import find_mxnet, fit
File "/tmp/mxnet/common/find_mxnet.py", line 4, in
import mxnet as mx
File "/tmp/mxnet/mxnet/__init__.py", line 7, in
from .base import MXNetError
File "/tmp/mxnet/mxnet/base.py", line 46, in
_LIB = _load_lib()
File "/tmp/mxnet/mxnet/base.py", line 38, in _load_lib
lib = ctypes.CDLL(lib_path[0], ctypes.RTLD_GLOBAL)
File "/usr/lib/python2.7/ctypes/__init__.py", line 365, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libcblas.so.3: cannot open shared object file: No such file or directory

Any Idea?

[max246]

To solve this issue you have to install libatlas-base-dev

sudo apt-get install libatlas-base-dev

[szha]

This issue is closed due to lack of activity in the last 90 days. Feel free to ping me to reopen if this is still an active issue. Thanks!

[anirudhacharya]

Using OS - "Linux ip-172-31-7-81 4.9.76-3.78.amzn1.x86_64" and python 2.7.
Tried -

import mxnet as mx
Traceback (most recent call last):
File "", line 1, in
File "/usr/local/lib/python2.7/site-packages/mxnet/__init__.py", line 25, in
from . import engine
File "/usr/local/lib/python2.7/site-packages/mxnet/engine.py", line 23, in
from .base import _LIB, check_call
File "/usr/local/lib/python2.7/site-packages/mxnet/base.py", line 111, in
_LIB = _load_lib()
File "/usr/local/lib/python2.7/site-packages/mxnet/base.py", line 103, in _load_lib
lib = ctypes.CDLL(lib_path[0], ctypes.RTLD_LOCAL)
File "/usr/lib64/python2.7/ctypes/__init__.py", line 357, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libgfortran.so.3: cannot open shared object file: No such file or directory

[ec2-user@ip-172-31-7-81 ~]$ sudo yum install libatlas-base-dev
Loaded plugins: priorities, update-motd, upgrade-helper
amzn-main | 2.1 kB 00:00:00
amzn-updates | 2.5 kB 00:00:00
No package libatlas-base-dev available.
Error: Nothing to do

But not able to use mxnet on this instance.

[szha]

@anirudhacharya for missing libgfortran.so.3 you need gfortran package instead of atlas.

[anirudhacharya]

@szha yum does not have gfortran just like libatlas-base-dev.
$ sudo yum install gfortran
Loaded plugins: priorities, update-motd, upgrade-helper
No package gfortran available.
Error: Nothing to do

[szha]

yum has a subcommand to help you find the file you need, yum provides libgfortran.so.3. The output tells you which package to install.

[anirudhacharya]

@szha
$ yum provides libgfortran.so.3
Loaded plugins: priorities, update-motd, upgrade-helper
libgfortran-4.4.6-4.81.amzn1.i686 : Fortran runtime
Repo : amzn-main
Matched from:
Provides : libgfortran.so.3

libgfortran-4.8.5-11.135.amzn1.i686 : Fortran runtime
Repo : amzn-main
Matched from:
Provides : libgfortran.so.3

libgfortran-6.4.1-1.45.amzn1.i686 : Fortran runtime
Repo : amzn-main
Matched from:
Provides : libgfortran.so.3

libgfortran-6.4.1-1.45.amzn1.i686 : Fortran runtime
Repo : @amzn-main
Matched from:
Provides : libgfortran.so.3

I installed the above package -
$ sudo yum install libgfortran-6.4.1-1.45.amzn1.i686

But when I try to import mxnet it still gives the same error -

import mxnet as mx
Traceback (most recent call last):
File "", line 1, in
File "/usr/local/lib/python2.7/site-packages/mxnet/__init__.py", line 25, in
from . import engine
File "/usr/local/lib/python2.7/site-packages/mxnet/engine.py", line 23, in
from .base import _LIB, check_call
File "/usr/local/lib/python2.7/site-packages/mxnet/base.py", line 111, in
_LIB = _load_lib()
File "/usr/local/lib/python2.7/site-packages/mxnet/base.py", line 103, in _load_lib
lib = ctypes.CDLL(lib_path[0], ctypes.RTLD_LOCAL)
File "/usr/lib64/python2.7/ctypes/__init__.py", line 357, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libgfortran.so.3: cannot open shared object file: No such file or directory

[anirudhacharya]

Also for the following packages, I am not able to find corresponding yum packages - liblapack-dev, liblas-dev, gfortran. I could usually install these packages with apt-get but yum is not able to find them.

$ sudo yum provides liblapack-dev
Loaded plugins: priorities, update-motd, upgrade-helper
No matches found
$ sudo yum provides liblas-dev
Loaded plugins: priorities, update-motd, upgrade-helper
No matches found
$ sudo yum provides gfortran
Loaded plugins: priorities, update-motd, upgrade-helper
No matches found

[anirudhacharya]

The AMI images of AWS does not have these packages. Installing them worked.
sudo yum -y install gcc-c++
sudo yum -y install gcc-gfortran
sudo yum -y install blas
sudo yum -y install lapack
sudo yum -y install atlas-sse3-devel

Thanks.

[iGEM-Thessaloniki-2019]

In Ubuntu 18.04, the following error:

sander: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

was fixed by running

sudo apt-get install libgfortran3:amd64

Also, in place of amd64 the I am aware of the following options: i386, i586, i686, x86_64.