trouble with installation in Linux

[David Hoover]

I've tried installing emspring both with the binary script and manual script.  We are running CentOS6.  I hit three errors that tank the procedure.

The first problem is at the step where it attempts to create a virtual environment for EMAN2.  It hits an infinite loop and then fails with this error:

RuntimeError: maximum recursion depth exceeded

The second problem is when it is fetching gcc:

RuntimeError: Can't retrieve url https://ftp.gnu.org/gnu/gcc/gcc-5.3.0/gcc-5.3.0.tar.bz2

Does emspring need gcc v5.3.0?

The last problem is when it attempts to install ipython:

ValueError: too many values to unpack

An error occurred when trying to install /tmp/tmpMFTGniget_dist/ipython-0.10.tar.gz. Look above this message for any errors that were output by easy_install.

Is there a more basic way of installing emspring?  We are using Anaconda as our python package manager.  I can create a virtual environment of almost any collection of versions.  What are the specific versions required for emspring?  In addition, we already have EMAN2 and SPARX installed locally.  Is there a simple way of simply tying them together?  Since python is provided with EMAN2, is there any reason to have python installed in the first place?

[David Hoover]

After tinkering a bit, I have some more solid suggestions.  The buildout_linux.cfg file attempts to download blas.tgz as version 3.5.0.  Unfortunately, the default version of blas is 3.7.0, and so the buildout breaks.  I needed to alter this to explicitly download blas-3.5.0.tgz.

[Carsten Sachse]

Dear David,

On Monday, 24 April 2017 21:11:44 UTC+2, David Hoover wrote:

I've tried installing emspring both with the binary script and manual script.  We are running CentOS6.  I hit three errors that tank the procedure.

 

The first problem is at the step where it attempts to create a virtual environment for EMAN2.  It hits an infinite loop and then fails with this error:

RuntimeError: maximum recursion depth exceeded

The second problem is when it is fetching gcc:

RuntimeError: Can't retrieve url https://ftp.gnu.org/gnu/gcc/gcc-5.3.0/gcc-5.3.0.tar.bz2

Does emspring need gcc v5.3.0?

The last problem is when it attempts to install ipython:

ValueError: too many values to unpack

An error occurred when trying to install /tmp/tmpMFTGniget_dist/ipython-0.10.tar.gz. Look above this message for any errors that were output by easy_install.

All of the above suggests to me some connectivity issue.

Is there a more basic way of installing emspring?  We are using Anaconda as our python package manager.  I can create a virtual environment of almost any collection of versions.  What are the specific versions required for emspring?  In addition, we already have EMAN2 and SPARX installed locally.  Is there a simple way of simply tying them together?  Since python is provided with EMAN2, is there any reason to have python installed in the first place?

As Spring has significantly more dependencies than EMAN2/sparx the process is rather tedious. In short current Spring code relies on the EMAN2/sparx code from 2013. Therefore, we use the respective binary from 2013 as a starting point. This in turn creates all issues of new building of scipy and numpy etc.

In case you come with a simpler approach eg. using anaconda and the latest EMAN2/sparx, I would be more than happy to use this.

Thanks for all your input.

Best wishes,

Carsten

[David Hoover]

I worked the problems like this:

1. The issue with virtual env was solved by avoiding it.  I installed the latest setuptools and skipped the virtualenv step by installing everything in the same python site-packages area as EMAN2.

2. Yes, the problem was connectivity.  I pre-fetched all the tarballs into the fetch directory.  In addition, I modified the buildout.cfg so that blas-3.5.0 instead of 3.7.0 was used.  I also had to switch to another computer with different connectivity to install the python modules in the last stage.

3. ipython-0.10 never worked no matter what.  So I commented out that step from the springpython section of the buildout.cfg and installed it manually into python using python setup.py install.

I've been able to get spring started, but not on every node in our cluster.  Sometimes when I launch the spring executable, it spins at 100% CPU load but never starts the GUI.  Any idea why it will just spin like that?  Attaching strace gives nothing.  I have to send it a kill signal to stop it.

[Carsten Sachse]

Dear David,

Thanks for the update and sharing your strategy. 

On Wednesday, 26 April 2017 01:11:23 UTC+2, David Hoover wrote:

I worked the problems like this:

1. The issue with virtual env was solved by avoiding it.  I installed the latest setuptools and skipped the virtualenv step by installing everything in the same python site-packages area as EMAN2.

 

Indeed that approach should also work. All components of EMAN2/sparx and Spring are now located and mixed in one library. 

2. Yes, the problem was connectivity.  I pre-fetched all the tarballs into the fetch directory.  In addition, I modified the buildout.cfg so that blas-3.5.0 instead of 3.7.0 was used.  I also had to switch to another computer with different connectivity to install the python modules in the last stage.

3. ipython-0.10 never worked no matter what.  So I commented out that step from the springpython section of the buildout.cfg and installed it manually into python using python setup.py install.

I've been able to get spring started, but not on every node in our cluster.  Sometimes when I launch the spring executable, it spins at 100% CPU load but never starts the GUI.  Any idea why it will just spin like that?  Attaching strace gives nothing.  I have to send it a kill signal to stop it.

Is it just the Spring GUI or are command line programs affected as well? In case you don't have libpng12.so.0 installed in your systems library, there are problems being reported.

Could the different behavior of different nodes explained by a missing library?

Best wishes,

Carsten 

[David Hoover]

No, libpng12.so.0 is available everywhere.  That's not the issue.  What command line programs should I test?

How should I know what libraries are missing?  Why would the program stall rather than crash due to missing libraries?

[David Hoover]

I've worked out the conditions for the stalling.  We are running the Slurm batch system.  When I allocate a node with more than one cpu, spring stalls.  If there is only one cpu, spring starts up the GUI and I can run through the examples.

On Wednesday, April 26, 2017 at 5:20:32 AM UTC-4, Carsten Sachse wrote: