Segmentation fault wannier 90 abinit 7.6.3

lorenzodona · Post by **lorenzodona** » Wed Apr 23, 2014 6:00 pm

Dear Abinit developers and users:
I compiled abinit 7.6.3 with this configuration setup:
./configure --enable-mpi=yes --with-mpi-prefix=/opt/local FCFLAGS_OPTIM="-g -O3 -Wl,-search_paths_first" CXXFLAGS="-g -O3 -Wl,-search_paths_first" --enable-zdot-bugfix=yes --enable-optim=safe -with-mpi-level=1 --enable-mpi-io=yes -with-dft-flavor="atompaw+bigdft+libxc+wannier90"
like abinit 7.6.2 and found no error when I run wannier 90 in abinit 7.6.2
but in version 7.6.3 i found this error in wannier 90:
Status file, reporting on built-in test libxc

==> The run finished cleanly.
Moreover, comparison of the total energy, and other (few) relevant quantities with reference values has been successful.
This does not mean that no problem is present, however.
Please run the complete set of ABINIT tests to gain a better confidence in your installation.

echo "Running built-in test in_wannier90"
Running built-in test in_wannier90
timeout="0" perl ./Scripts/run-basic-tests.pl built-in in_wannier90 /Users/lorenzodona/Documents/abinit-7.6.3/tests

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

Backtrace for this error:
#0 0x11209b70d
#1 0x11209bc1b
#2 0x7fff945815a9
#3 0x7fff8b05f03a
#4 0x10da05321
#5 0x10da0f2d1
#6 0x10d0cec5f
#7 0x10cbf9c48
#8 0x10cc188fc
#9 0x10cc23d11
#10 0x10cc24447
#11 0x10cbc4ff3
#12 0x10cbcc371
#13 0x10cbb061e
#14 0x10cb97548
#15 0x10ddc87ce
sh: line 1: 59895 Segmentation fault: 11 ../../../src/98_main/abinit < testin_wannier90.files > testin_wannier90.log

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

Status file, with repetition rate 49, status number 10

Level abinit : call macroin2

and also when i run:
untests.py wannier90 i found a lots of errors like this:
[wannier90][t03] fldiff.pl fatal error:
The diff analysis cannot be done : the number of lines to be analysed differ.
File /Users/lorenzodona/Documents/abinit-7.6.3/tests/wannier90/Refs/t03.out: 2382 lines, 131 ignored
File /Users/lorenzodona/Documents/abinit-7.6.3/tests/Test_suite/wannier90_t03/t03.out: 2381 lines, 131 ignored

Please can you help me to solve this problem?
thank again for your patience with me.
Dearly lorenzo
thanks again:

Post by **pouillon** » Fri Apr 25, 2014 11:25 am

Which compiler and version are you using?

lorenzodona · Post by **lorenzodona** » Fri Apr 25, 2014 7:57 pm

Dear pouillon thanks really to help me i use to compile abinit gcc 4.8.2
GNU Fortran (GCC) version 4.8.2 (x86_64-apple-darwin13)
I added the config file

Post by **pouillon** » Mon Apr 28, 2014 11:15 am

Could you rebuild Abinit after putting the following in your config file and let us know if it changes something?

Code: Select all

fcflags_opt_67_common="-O2"
fcflags_opt_77_lwf="-O2"
fcflags_opt_wannier90="-O2"

If not, could you try with "-O1" and with "-O0" as well?

lorenzodona · Post by **lorenzodona** » Mon Apr 28, 2014 2:59 pm

Dear pouillon thanks really to help me but it doesn't work with every value of flags -O2 -O1 and -O0
thanks again

Post by **pouillon** » Tue May 06, 2014 6:58 pm

To be fully sure: could you build after configuring with the following options?

Code: Select all

--enable-optim="no" --enable-debug="enhanced"

gmatteo · Post by **gmatteo** » Wed May 07, 2014 1:03 am

I have the feeling that the problem is due to VECLIB (Apple's version of BLAS and LAPACK).

Could you run wannier.x in the GNU debugger gdb:

# To start the debugger:
$ gdb path_to_abinit

# To start the applications:
gdb_prompt> run < testin_wannier90.files

... SEGMENTATION FAULT ...
# Use the backtrace command to get the list of calls and post the output.
gdb_prompt> backtrace

You may want to reduce the optimization level (-O3 --> -O2) to get more useful and reliable information from gdb.

lorenzodona · Post by **lorenzodona** » Wed May 28, 2014 10:36 am

Thanks to everyone and excuse me for my delay but I have a lot of things to study
Dearly lorenzo I solved also the problem with export the wannier90 bin dir and wannier90 compiled by myself..
thanks thanks a lot.

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