Installing lsst_sims on ubuntu 14.04.5 fails

Support
#1

Hi all,

I’m trying to install from source the lsst_sims and I got the error below.
Do you know how I can fix it?

thanks in advance
Stefano

  [ 61/88 ]  daf_persistence 13.0-8-gba0f85f+1 ... 

***** error: from /dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/build.log:
  File "/dark/usr/lsst_stack/Linux64/miniconda2/4.2.12.lsst1/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/python/lsst/daf/persistence/safeFileIo.py", line 123, in SafeFilename
    temp = tempfile.NamedTemporaryFile(mode="w", dir=outDir, prefix=outName, delete=False)
  File "/dark/usr/lsst_stack/Linux64/miniconda2/4.2.12.lsst1/lib/python2.7/tempfile.py", line 475, in NamedTemporaryFile
    (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags)
  File "/dark/usr/lsst_stack/Linux64/miniconda2/4.2.12.lsst1/lib/python2.7/tempfile.py", line 244, in _mkstemp_inner
    fd = _os.open(file, flags, 0600)
OSError: [Errno 2] No such file or directory: '/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/tests/root/out/foo3.pickleDUXidT'
----------------------------------------------------------------------
Ran 5 tests in 0.081s

FAILED (errors=1)
The following tests failed:
/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/tests/.tests/mapperImport.py.failed
1 tests failed
scons: *** [checkTestStatus] Error 1
scons: building terminated because of errors.
+ exit -4
eups distrib: Failed to build daf_persistence-13.0-8-gba0f85f+1.eupspkg: Command:
        source /dark/usr/lsst_stack/eups/bin/setups.sh; export EUPS_PATH=/dark/usr/lsst_stack; (/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/build.sh) >> /dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/build.log 2>&1 4>/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/build.msg 
exited with code 252
#2

Hi Stefano, can you add more information about your python setup - are you using the miniconda installed by newinstall.sh and did you upgrade any of those packages (or the python itself) prior to installing the rest of the packages (before eups distrib install lsst_sims -t sims)

#3

Oh and also please include the contents of
/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/tests/.tests/mapperImport.py.failed

#4

What kind of filesystem are you running this on?

#5

I’m using the miniconda installed by newinstall.sh following the instruction from here: https://pipelines.lsst.io/install/newinstall.html

#6

I think it’s a race condition in daf_persistence: DM-10352.

#7

Yes, I think you’re right. I was discounting the possibility of race conditions because it’s a temp file, but I forgot about the directory problem.

The good news is that it will probably magically work if you try again. If it doesn’t, try over with EUPS_SCONSFLAGS="-j 1" (only necessary until you get past daf_persistence).

#8

Here is the mapperImport.py.failed

I will now try to run it again as suggested by Paul

E…

ERROR: testIO (main.MapperImportTestCase)

Traceback (most recent call last):
File “tests/mapperImport.py”, line 66, in testIO
self.checkIO(self.butler, bbox, 3)
File “tests/mapperImport.py”, line 58, in checkIO
butler.put(bbox, “x”, ccd=ccd)
File “/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/python/lsst/daf/persistence/butler.py”, line 1004, in put
location.getRepository().write(location, obj)
File “/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/python/lsst/daf/persistence/repository.py”, line 184, in write
return butlerLocationStorage.write(butlerLocation, obj)
File “/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/python/lsst/daf/persistence/posixStorage.py”, line 303, in write
with SafeFilename(os.path.join(self.root, locations[0])) as locationString:
File “/dark/usr/lsst_stack/Linux64/miniconda2/4.2.12.lsst1/lib/python2.7/contextlib.py”, line 17, in enter
return self.gen.next()
File “/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/python/lsst/daf/persistence/safeFileIo.py”, line 123, in SafeFilename
temp = tempfile.NamedTemporaryFile(mode=“w”, dir=outDir, prefix=outName, delete=False)
File “/dark/usr/lsst_stack/Linux64/miniconda2/4.2.12.lsst1/lib/python2.7/tempfile.py”, line 475, in NamedTemporaryFile
(fd, name) = _mkstemp_inner(dir, prefix, suffix, flags)
File “/dark/usr/lsst_stack/Linux64/miniconda2/4.2.12.lsst1/lib/python2.7/tempfile.py”, line 244, in _mkstemp_inner
fd = _os.open(file, flags, 0600)
OSError: [Errno 2] No such file or directory: ‘/dark/usr/lsst_stack/EupsBuildDir/Linux64/daf_persistence-13.0-8-gba0f85f+1/daf_persistence-13.0-8-gba0f85f+1/tests/root/out/foo3.pickleDUXidT’

Ran 5 tests in 0.081s

FAILED (errors=1)

#9

running again the installation succeeded!
thanks for the help