UnixConnection.py has a problem in osx.

[yumyai]

I am trying TEES on mac (mountain lion). There is command that not compatible with tools on osx.

In Utils/Connection/UnixConnection.py: line 478. You used

for line in self.run("ps -p " + jobAttr["PID"] + " -o etime, --no-heading"):

A --no-heading option is not available for ps on osx. Changing that line to for line in self.run("ps -p " + jobAttr["PID"] + " -o etime,")[1:]: works well.

I only try with "python classify.py -m GE -i 9668063 -o OUTSTEM" job though.

[renaud]

Thanks Jari for sharing your code.

I can confirm the above issue on OS X. I fixed it like this

for line in self.run("ps -p " + jobAttr["PID"] + " -o etime=\"\" "):

Also, I had to add some memory to BANNER to make it work.

--- a/Tools/BANNER.py
+++ b/Tools/BANNER.py
@@ -248,9 +248,9 @@ def run(input, output=None, elementName="entity", processElement="document", spl
 cwd = os.getcwd()
 os.chdir(bannerPath)
 if oldVersion: # old version
-        args = ["java", "-cp", classPath, "banner.eval.TestModel", config]
+        args = ["java", "-Xms1G", "-Xmx2G", "-cp", classPath, "banner.eval.TestModel", config]
 else:
-        args = ["java", "-cp", classPath, "banner.eval.BANNER", "test", config]
+        args = ["java", "-Xms1G", "-Xmx2G", "-cp", classPath, "banner.eval.BANNER", "test", config]
 print >> sys.stderr, "BANNER command:", " ".join(args)```

[jbjorne]

Thank you for the bug reports!

I've fixed the issue with the OS X ps command using yumyai's suggestion, by removing the --no-heading switch and reading the output lines starting from 1.

As for the java memory issue, I added a "JAVA" parameter to the configuration settings. By default this is just the "java" command, but to define your own java settings, you can override it in ".tees_local_settings.py" (or whatever file you use for local settings). E.g. for the memory error mentioned by renaud, you would add to the local settings file the line:

JAVA = "java -Xms1G -Xmx2G"

The JAVA setting could also be used to point to a non-standard java installation not in the path etc.

Both updates have been pushed to the main TEES repository. Hopefully these fixes will solve the issues mentioned!

[renaud]

Thanks Jari!