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Created by Podhorszki, Norbert@pnbOwner

summit anaconda build error

Created by: zeneofa

Hi,

I am having problems trying to build adios2 on summit, using the anaconda environment. I seems that the adios2.cpython-36m-powerpc64le-linux-gnu.so file is not created all. I am building from the github master branch

╰─[:)] % git rev-parse HEAD
cbaf8ca92b4550cad603522e6570f3cbf95acdba

The modules that I have loaded:

Currently Loaded Modules:
  1) hsi/5.0.2.p5   3) lsf-tools/2.0           5) DefApps         7) python/3.6.6-anaconda3-5.3.0   9) cmake/3.14.2                    11) magma/2.3.0
  2) xalt/1.1.3     4) darshan-runtime/3.1.7   6) cuda/10.1.105   8) gcc/6.4.0                     10) spectrum-mpi/10.3.0.0-20190419

I use the following command to build

mkdir adios2-build
cd adios2-build
cmake -DCMAKE_C_COMPILER=${OMPI_CC} -DCMAKE_CXX_COMPILER=${OMPI_CXX} -DCMAKE_INSTALL_PREFIX=~/software/adios2 -DADIOS2_USE_Fortran=OFF -DADIOS2_USE_ZeroMQ=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DADIOS2_USE_SST=OFF .. 2>&1 | tee cmake.configure.adios2.log

After this I run

make -j 1 2>&1 | tee  make.adios2.log

which then errors with:

[ 38%] Building CXX object bindings/Python/CMakeFiles/adios2py.dir/py11glue.cpp.o
[ 39%] Linking CXX shared module ../../lib64/python3.6/site-packages/adios2.cpython-36m-powerpc64le-linux-gnu.so
lto1: internal compiler error: invalid line in the resolution file
0x101d225b lto_resolution_read
	/sw/summit/gcc/6.4.0/src/gcc-6.4.0/gcc/lto/lto.c:1912
0x101d225b lto_file_read
	/sw/summit/gcc/6.4.0/src/gcc-6.4.0/gcc/lto/lto.c:2092
0x101d225b read_cgraph_and_symbols
	/sw/summit/gcc/6.4.0/src/gcc-6.4.0/gcc/lto/lto.c:2806
0x101d225b lto_main()
	/sw/summit/gcc/6.4.0/src/gcc-6.4.0/gcc/lto/lto.c:3310
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <http://gcc.gnu.org/bugs.html> for instructions.
lto-wrapper: fatal error: /sw/summit/gcc/6.4.0/bin/g++ returned 1 exit status
compilation terminated.
/usr/bin/ld: error: lto-wrapper failed
/usr/bin/sha1sum: ../../lib64/python3.6/site-packages/adios2.cpython-36m-powerpc64le-linux-gnu.so: No such file or directory
collect2: error: ld returned 1 exit status
make[2]: *** [lib64/python3.6/site-packages/adios2.cpython-36m-powerpc64le-linux-gnu.so] Error 1
make[1]: *** [bindings/Python/CMakeFiles/adios2py.dir/all] Error 2
make: *** [all] Error 2

I have loaded the output logs on gist here: https://gist.github.com/zeneofa/9c6d8ccb102a8c21f45032dfce29846a

This seems to be anaconda specific, as when I use the standard python module I do not get the lto error.

module unload python/3.6.6-anaconda3-5.3.0
module load python/3.7.0

This is independent of python version, using the anaconda 3.7 version also fails.

Any help would be much appreciated. Thanks in advance.

P