Closed gijzelaerr closed 5 years ago
ok to test
Looks like a bug in the latest casacore:
creating new column BITFLAG_ROW using an IncrementalStMan storage manager
DATA column storage manager type is StandardStMan
BITFLAG column will use a default storage manager
Adding BITFLAG column with fixed shape: [4, 64]
2018/05/29 08:07:45 ABORT: /usr/local/bin/addbitflagcol returned error code -11
2018/05/29 08:07:45 ERROR: exiting with error code 1, check the logs for errors
2018/05/29 08:07:45 INFO: elapsed time is 0h0m1.26s
========== Removing files
========== $ rm -fr WSRT.MS* WSRT*img WSRT*fits
========== Running makems
========== $ makems /code/test/Batchtest/WSRT_makems.cfg
========== $ mv WSRT.MS_p0 WSRT.MS
========== $ pyxis WSRT.MS ms.prep
Traceback (most recent call last):
File "batch_test.py", line 92, in <module>
run("pyxis WSRT.MS ms.prep"); #TODO: this is hacky, bug in CASAcore
File "batch_test.py", line 30, in run
raise RuntimeError,"failed with exit code %x"%code;
RuntimeError: failed with exit code 1
Its addColumn that is segfaulting
#0 0x00007ffff72a138a in casa::SSMBase::removeColumn(casa::DataManagerColumn*) () from /usr/lib/x86_64-linux-gnu/libcasa_tables.so.2
#1 0x00007ffff7194901 in casa::ColumnSet::doAddColumn(casa::ColumnDesc const&, casa::DataManager*) ()
from /usr/lib/x86_64-linux-gnu/libcasa_tables.so.2
#2 0x00007ffff7196f49 in casa::ColumnSet::addColumn(casa::ColumnDesc const&, bool, casa::TSMOption const&, casa::Table&) ()
from /usr/lib/x86_64-linux-gnu/libcasa_tables.so.2
#3 0x00007ffff71b6f4a in casa::PlainTable::addColumn(casa::ColumnDesc const&, bool) ()
from /usr/lib/x86_64-linux-gnu/libcasa_tables.so.2
#4 0x000055555555948b in main ()
can't replicate the problem with the KERN package of meqtrees, maybe it is MS specific
$ /usr/bin/addbitflagcol meerkat_0h10s.MS
creating new column BITFLAG_ROW using an IncrementalStMan storage manager
DATA column storage manager type is TiledShapeStMan
BITFLAG column will use a default storage manager
Adding BITFLAG column with variable shape
Initializing variable-shaped BITFLAG column
$ dpkg -S /usr/bin/addbitflagcol
meqtrees-timba: /usr/bin/addbitflagcol
$ apt-cache show meqtrees-timba:
Package: meqtrees-timba
Priority: extra
Section: science
Installed-Size: 408
Maintainer: KERN packaging <packaging@kernsuite.info>
Architecture: amd64
Version: 1.5.1-1kern1
Depends: libc6 (>= 2.14), libcasa-casa2, libcasa-images2, libcasa-measures2, libcasa-ms2, libcasa-msfits2, libcasa-tables2, libcfitsio5 (>= 3.390~), libfftw3-double3 (>= 3.3.5), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2), libwcs5 (>= 4.8.2), python-meqtrees-timba, libmeqtrees-timba0, casarest, python2.7
Filename: pool/main/m/meqtrees-timba/meqtrees-timba_1.5.1-1kern1_amd64.deb
Size: 100424
MD5sum: 995af5815755242ee3c0a93bfd9ab994
SHA1: a322ae70d1c61e3bdeeaae45838c4fab747b8370
SHA256: 1296c57543e31ff3edc65c624840e741ef5ec82aef38c2d38fff81901276cb89
Description-en: implementing and solving arbitrary Measurement Equations
MeqTrees is a software package for implementing Measurement Equations. This
makes it uniquely suited for simulation and calibration of radioastronomical
data, especially that involving new radiotelescopes and observational
regimes.
.
MeqTrees includes a highly capable FITS viewer and sky model manager called
Tigger, which can also work as a standalone tool.
Description-md5: 72e294c70ac8c86e7edccfb79c0b1b96
$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=18.04
DISTRIB_CODENAME=bionic
DISTRIB_DESCRIPTION="Ubuntu 18.04 LTS"
linkage looks okay:
root@6a5b7c27dc5d:/code/test/Batchtest# ldd /usr/lib/x86_64-linux-gnu/libcasa_tables.so.2
linux-vdso.so.1 (0x00007ffec51f2000)
libcasa_casa.so.2 => /usr/lib/x86_64-linux-gnu/libcasa_casa.so.2 (0x00007faa04565000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007faa041d7000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007faa03e39000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007faa03c21000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007faa03a02000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007faa03611000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007faa0340d000)
/lib64/ld-linux-x86-64.so.2 (0x00007faa0539a000)
maybe it is lofar's makems that is the problem
maybe time to switch to writems
The segfault is in the latest casacore (master).. will try and reproduce with latest release to double check
also there in CC 2.4.0. I can only conclude it it is a LOFAR makems problem
@gijzelaerr can you elaborate on what is wrong with the makems build?
https://github.com/kernsuite/packaging/issues/103 https://github.com/ska-sa/makems/issues/3
I prefer to ditch it completely. Can you switch to writems which is now part of casacore?
otherwise, @Athanaseus could try to fix the upstream makems pacakge and role a new debian package for kern-dev (4)
superseded by recent work
Can one of the admins verify this patch?