[GSAS-II] problem installing gsas2 on linux server
Long Yang
dragonyang92 at gmail.com
Mon May 4 15:13:51 CDT 2020
Hi Brian,
Thanks for your suggestion. After a long journey, I kind of found a temporary solution to install. The problem is from, as you pointed out, the `wx` package on linux. I wrote my solution below and share with the community in case anyone have similar problem when conda install gsas2.
1. conda install wxpython #it will install 4.0.4 version on my case
2. go to ~/anaconda.../lib/python3.7/site-packages/wx/__init__.py
comment out all the lines within the file, and manually add `__version__=“4.0.4”`
3. conda install gsas2pkg -c briantoby #now, the bootstrap.py error finally passes. and in my case, GSASII is installed successfully now.
4. go to ~/anaconda.../lib/python3.7/site-packages/wx/__init__.py
uncomment the lines did in step 2, but leave `__version__=“4.0.4”` there, and still comment out `import wx.__version__` line, otherwise, similar error will happen again every time calling the GSASII bootstrap.py.
In this way, I can use GSASIIscriptable without problem, I am not using GUI on the linux server, so I didn’t check whether this solution will cause any problem on GSASII GUI.
Thanks!
Long
> On May 4, 2020, at 3:21 PM, Toby, Brian H. <toby at anl.gov> wrote:
>
> 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 <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$
>>
>> _______________________________________________
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>
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