[GSAS-II] problem installing gsas2 on linux server
Toby, Brian H.
toby at anl.gov
Mon May 4 14:21:10 CDT 2020
Hi Long,
The error message you show:
Traceback (most recent call last):
File "/opt/anaconda/miniconda3/envs/gsas/GSASII/bootstrap.py", line 187, in <module>
exec('import '+pkg)
File "<string>", line 1, in <module>
File "/opt/anaconda/miniconda3/envs/gsas/lib/python3.7/site-packages/wx/__init__.py", line 12, in <module>
__version__ = wx.__version__.VERSION_STRING
AttributeError: module 'wx' has no attribute '__version__'
seems to show that wx is installed, but is not functioning properly. I think that using import wx from inside python will demonstrate this. Installation into Linux is turning into a big challenge. I think this is because there are so many dists with different vintages of libraries.
I am only going to be of limited help with this, but I am concerned that you have mentioned you both used conda and pip to install wx. That could be a problem and you might need to clear house and reinstall python. You might do some research to see if there is some extra ubuntu package (glib or something like that?) that is needed to make this work. Alternately, you might want to install ubuntu python and the packages we need via the Ubuntu. I think I have done that in Ubuntu a few years ago, so I think this works too.
You do not need to use GSAS-II as a diagnostic, start by seeing if you can get to the point where "import wx” works in python. Once you have that, you can test with GSAS-II using
<path>python /opt/anaconda/miniconda3/envs/gsas/GSASII/GSASII.py
once that works, take a look at the /opt/anaconda/miniconda3/envs/gsas/GSASII/makeLinux.py
script to see if you want what that does (it could use some input from dedicated Linux users FWIW.)
Brian
On May 4, 2020, at 12:39 PM, Long Yang via GSAS-II <gsas-ii at aps.anl.gov<mailto:gsas-ii at aps.anl.gov>> wrote:
Hi,
I met a problem when conda install gsas2 on an Ubuntu (18.04.3 LTS) server machine. When `conda install gsas2pkg -c briantoby`, it seems like always stuck at running the bootstrap saying not finding `wx` package. I pasted the error log in the bottom. python version is 3.7.3, and I have no such problem conda install gsas2 on my mac machine before.
I tried to conda install and pip install the wxpython first, and I am making sure that I have wxpython 4.0.4 inside my conda environment, then install gsas2, but still same error.
I also tried to download the `gsas2full-Latest-Linux-x86_64.sh` following instruction at https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/LinuxSingleStepInstaller, but after installation, in the `gsas2full` folder, I didn’t find a `GSASII` folder as step 4 said.
BTW, this linux machine is inside national lab firewall, not sure if this causes a problem.
Thanks!
Long Yang
full error log:
(gsas) anaconda at addie:~/GSASII$ conda install gsas2pkg -c briantoby
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /opt/anaconda/miniconda3/envs/gsas
added / updated specs:
- gsas2pkg
The following NEW packages will be INSTALLED:
apr pkgs/main/linux-64::apr-1.6.3-he40df45_0
asn1crypto pkgs/main/linux-64::asn1crypto-1.3.0-py37_0
blas pkgs/main/linux-64::blas-1.0-mkl
cffi pkgs/main/linux-64::cffi-1.14.0-py37h2e261b9_0
chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003
conda pkgs/main/linux-64::conda-4.8.3-py37_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
cycler pkgs/main/linux-64::cycler-0.10.0-py37_0
cyrus-sasl pkgs/main/linux-64::cyrus-sasl-2.1.26-h82bf5a1_4
dbus pkgs/main/linux-64::dbus-1.13.12-h746ee38_0
gsas2pkg briantoby/linux-64::gsas2pkg-1.0.6-0
h5py pkgs/main/linux-64::h5py-2.10.0-py37h7918eee_0
hdf5 pkgs/main/linux-64::hdf5-1.10.4-hb1b8bf9_0
idna pkgs/main/noarch::idna-2.9-py_1
imageio pkgs/main/noarch::imageio-2.8.0-py_0
intel-openmp pkgs/main/linux-64::intel-openmp-2020.0-166
kiwisolver pkgs/main/linux-64::kiwisolver-1.2.0-py37hfd86e86_0
krb5 pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0
libdb pkgs/main/linux-64::libdb-6.1.26-he6710b0_0
libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
libntlm pkgs/main/linux-64::libntlm-1.5-h7b6447c_0
libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_0
libutf8proc pkgs/main/linux-64::libutf8proc-2.1.1-h14c3975_0
lz4-c pkgs/main/linux-64::lz4-c-1.8.1.2-h14c3975_0
matplotlib pkgs/main/linux-64::matplotlib-3.1.3-py37_0
matplotlib-base pkgs/main/linux-64::matplotlib-base-3.1.3-py37hef1b27d_0
mkl pkgs/main/linux-64::mkl-2020.0-166
mkl-service pkgs/main/linux-64::mkl-service-2.3.0-py37he904b0f_0
mkl_fft pkgs/main/linux-64::mkl_fft-1.0.15-py37ha843d7b_0
mkl_random pkgs/main/linux-64::mkl_random-1.1.0-py37hd6b4f25_0
numpy pkgs/main/linux-64::numpy-1.18.1-py37h4f9e942_0
numpy-base pkgs/main/linux-64::numpy-base-1.18.1-py37hde5b4d6_1
olefile pkgs/main/linux-64::olefile-0.46-py37_0
pillow pkgs/main/linux-64::pillow-7.1.2-py37hb39fc2d_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopengl pkgs/main/linux-64::pyopengl-3.1.1a1-py37_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
pyparsing pkgs/main/noarch::pyparsing-2.4.7-py_0
pyqt pkgs/main/linux-64::pyqt-5.9.2-py37h05f1152_2
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0
python-dateutil pkgs/main/noarch::python-dateutil-2.8.1-py_0
qt pkgs/main/linux-64::qt-5.9.7-h5867ecd_1
requests pkgs/main/linux-64::requests-2.23.0-py37_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
scipy pkgs/main/linux-64::scipy-1.4.1-py37h0b6359f_0
serf pkgs/main/linux-64::serf-1.3.9-h1c830df_0
sip pkgs/main/linux-64::sip-4.19.8-py37hf484d3e_0
svn pkgs/main/linux-64::svn-1.10.2-h52f66ed_0
tornado pkgs/main/linux-64::tornado-6.0.4-py37h7b6447c_1
tqdm pkgs/main/noarch::tqdm-4.45.0-py_0
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py37_0
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2
zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link<http://conda.core.link>:_execute(700): An error occurred while installing package'briantoby::gsas2pkg-1.0.6-0'.
Rolling back transaction: done
LinkError: post-link script failed for package briantoby::gsas2pkg-1.0.6-0
location of failed script: /opt/anaconda/miniconda3/envs/gsas/bin/.gsas2pkg-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: Preparing to install GSAS-II from APS subversion server
/opt/anaconda/miniconda3/envs/gsas/bin/python
Running bootstrap from /opt/anaconda/miniconda3/envs/gsas/GSASII at 2020-05-04 13:26:16.993798
Id: $Id: bootstrap.py 3515 2018-07-30 02:14:14Z toby $
**********************************************************************
Preloading matplotlib to build fonts...
Checking python packages...
Sorry, this version of Python cannot be used
for GSAS-II. It is missing the following package(s):
wx
Please install these package(s) and try running this again.
Showing first error:
stderr: mkdir: cannot create directory ‘/opt/anaconda/miniconda3/envs/gsas/GSASII’: File exists
Traceback (most recent call last):
File "/opt/anaconda/miniconda3/envs/gsas/GSASII/bootstrap.py", line 187, in <module>
exec('import '+pkg)
File "<string>", line 1, in <module>
File "/opt/anaconda/miniconda3/envs/gsas/lib/python3.7/site-packages/wx/__init__.py", line 12, in <module>
__version__ = wx.__version__.VERSION_STRING
AttributeError: module 'wx' has no attribute '__version__'
return code: 1
()
(gsas) anaconda at addie:~/GSASII$
_______________________________________________
GSAS-II mailing list
GSAS-II at aps.anl.gov<mailto:GSAS-II at aps.anl.gov>
https://mailman.aps.anl.gov/mailman/listinfo/gsas-ii
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.aps.anl.gov/pipermail/gsas-ii/attachments/20200504/b32d8d3d/attachment-0001.html>
More information about the GSAS-II
mailing list