search

draeger-lab / SBSCL

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
https://draeger-lab.github.io/SBSCL/
GNU Lesser General Public License v3.0
20 stars 13 forks source link

FBA tests fail on parallel testing #51

Closed hemilpanchiwala closed 4 years ago

hemilpanchiwala commented 4 years ago

This issue occurs while testing the SBML models with FBC extension from the SBML Test Suite.

The main problem behind this seems to be due to the GLPK Solver. @matthiaskoenig also pointed out this:

Like mentioned in the discussion, the GLPK can probably not be run in parallel via threads. See http://glpk-java.sourceforge.net/usage.html:

The GLPK library is not thread safe. Never two threads should be running that access the GLPK library at the same time. When a new thread accesses the library it should call GLPK.glp_free_env(). When using an GlpkTerminalListener it is necessary to register GlpkTerminal again by calling GLPK.glp_term_hook(null, null).

The only reason why this works in the TestRunner is because it starts a separate Java program for every test.

hemilpanchiwala commented 4 years ago

@matthiaskoenig @draeger As now we know where the error was for this issue and it's resolved in the forked repository. So should I link this issue to the PR so that it closes on the merge of the PR?

matthiaskoenig commented 4 years ago

Yes, link the issue.

On Thu, Jul 2, 2020 at 11:06 AM Hemil Panchiwala notifications@github.com wrote:

@matthiaskoenig https://github.com/matthiaskoenig @draeger https://github.com/draeger As now we know where the error was for this issue and it's resolved in the forked repository. So should I link this issue to the PR so that it closes on the merge of the PR?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/draeger-lab/SBSCL/issues/51#issuecomment-652886129, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG33OTY7LGKKFCVPNGHJ2DRZREYHANCNFSM4OLCQXJQ .

-- Matthias König, PhD. Junior Group Leader LiSyM - Systems Medicine of the Liver Humboldt Universität zu Berlin, Institute of Biology, Institute for Theoretical Biology https://livermetabolism.com konigmatt@googlemail.com https://twitter.com/konigmatt https://github.com/matthiaskoenig Tel: +49 30 2093 98435