[Debichem-devel] Bug#925624: abinit: ftbfs with GCC-9

[Matthias Klose]

Package: src:abinit
Version: 8.8.4-2
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-9

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/abinit_8.8.4-2_unstable_gcc9.log
The last lines of the build log are at the end of this report.

To build with GCC 9, either set CC=gcc-9 CXX=g++-9 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-9/porting_to.html

GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.

[...]


YAML Error found in the stdout of [fast][t29][np=1]
--- !ERROR
src_file: inwffil.F90
src_line: 246
mpi_rank: 0
message: |
    Missing data file: t27o_WFK
...

Command   /<<PKGBUILDDIR>>/src/98_main/abinit < /<<PKGBUILDDIR>>/tests/Test_suite/fast_t30/t30.stdin > /<<PKGBUILDDIR>>/tests/Test_suite/fast_t30/t30.stdout 2> /<<PKGBUILDDIR>>/tests/Test_suite/fast_t30/t30.stderr
 returned exit_code: 139

[fast][t30][np=1]: fldiff.pl fatal error:
The diff analysis cannot be done: the number of lines to be analysed differ.
File /<<PKGBUILDDIR>>/tests/fast/Refs/t30.out: 399 lines, 44 ignored
File /<<PKGBUILDDIR>>/tests/Test_suite/fast_t30/t30.out: 397 lines, 43 ignored [file=t30.out]
[fast][t30][np=1]Test was not expected to fail but subprocesses returned 139

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7f063149eb40 in ???
#1  0x7f063149dd75 in ???
#2  0x7f063115893f in ???
#3  0x5612b98bb243 in forces_
	at /<<PKGBUILDDIR>>/src/67_common/forces.F90:462
#4  0x5612b98c136f in forstr_
	at /<<PKGBUILDDIR>>/src/67_common/forstr.F90:439
#5  0x5612b8ff7807 in afterscfloop_
	at /<<PKGBUILDDIR>>/src/94_scfcv/afterscfloop.F90:895
#6  0x5612b8febdd4 in scfcv_
	at /<<PKGBUILDDIR>>/src/94_scfcv/scfcv.F90:2078
#7  0x5612b8fcbd5b in scfcv_scfcv
	at /<<PKGBUILDDIR>>/src/94_scfcv/m_scfcv.F90:748
#8  0x5612b8fcc3/<<PKGBUILDDIR>>/tests/pymods/testsuite.py:3317: UserWarning: exception while adding /<<PKGBUILDDIR>>/tests/Test_suite/fast_t27-t28-t29/t29o_TIM8_GEO to tarball:
[Errno 2] No such file or directory: '/<<PKGBUILDDIR>>/tests/Test_suite/fast_t27-t28-t29/t29o_TIM8_GEO'
  warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/<<PKGBUILDDIR>>/tests/pymods/testsuite.py:3317: UserWarning: exception while adding /<<PKGBUILDDIR>>/tests/Test_suite/fast_t27-t28-t29/t28o_TIM2_GEO to tarball:
[Errno 2] No such file or directory: '/<<PKGBUILDDIR>>/tests/Test_suite/fast_t27-t28-t29/t28o_TIM2_GEO'
  warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
1e in __m_scfcv_MOD_scfcv_run
	at /<<PKGBUILDDIR>>/src/94_scfcv/m_scfcv.F90:531
#9  0x5612b8f74046 in gstate_
	at /<<PKGBUILDDIR>>/src/95_drive/gstate.F90:1239
#10  0x5612b8e6f7db in gstateimg_
	at /<<PKGBUILDDIR>>/src/95_drive/gstateimg.F90:520
#11  0x5612b8e49c99 in driver_
	at /<<PKGBUILDDIR>>/src/95_drive/driver.F90:670
#12  0x5612b8e39195 in abinit
	at /<<PKGBUILDDIR>>/src/98_main/abinit.F90:444
#13  0x5612b8e3d5ff in main
	at /<<PKGBUILDDIR>>/src/98_main/abinit.F90:95
Segmentation fault

No YAML Error found in [fast][t30][np=1]

Suite   failed  passed  succeeded  skipped  disabled  run_etime  tot_etime
fast        11       0          0        0         0      26.23      26.40

Completed in 27.21 [s]. Average time for test=2.38 [s], stdev=1.58 [s]
Summary: failed=11, succeeded=0, passed=0, skipped=0, disabled=0

Execution completed.
Results in HTML format are available in Test_suite/suite_report.html
make[1]: *** [debian/rules:79: override_dh_auto_test-arch] Error 11
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:15: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2