Hello,
I am attempting to build Rosetta but I am running into problems. Rosetta tries
to build libxml2 and using foss-2019b the include path contains the tool-chain
libxml2. An excerpt from the logs shows this problem:
mpicc -o
build/external/release/linux/3.10/64/x86/gcc/8.3/mpi-serialization/libxml2/list.os
-c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem
external/include/ -isystem external/dbio/ -isystem external/libxml2/include
-isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2
-mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops
-finline-functions -finline-limit=20000 -s -Wno-unused-variable
-Wno-unused-parameter -O2 -ftree-vectorize -march=native -fno-math-errno
-DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY
-DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS
-DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DSERIALIZATION -DNDEBUG
-DUSEMPI -DMPICH_IGNORE_CXX_SEEK -Iexternal/include
-I/opt/site/easybuild/software/ScaLAPACK/2.0.2-gompi-2019b/include
-I/opt/site/easybuild/software/FFTW/3.3.8-gompi-2019b/include
-I/opt/site/easybuild/software/OpenBLAS/0.3.7-GCC-8.3.0/include
-I/opt/site/easybuild/software/OpenMPI/3.1.4-GCC-8.3.0/include
-I/opt/site/easybuild/software/hwloc/1.11.12-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/libpciaccess/0.14-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/libxml2/2.9.9-GCCcore-8.3.0/include/libxml2
-I/opt/site/easybuild/software/libxml2/2.9.9-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/XZ/5.2.4-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/numactl/2.0.12-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/binutils/2.32-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/zlib/1.2.11-GCCcore-8.3.0/include
external/libxml2/list.c
mpicc -o
build/external/release/linux/3.10/64/x86/gcc/8.3/mpi-serialization/libxml2/nanoftp.os
-c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem
external/include/ -isystem external/dbio/ -isystem external/libxml2/include
-isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2
-mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops
-finline-functions -finline-limit=20000 -s -Wno-unused-variable
-Wno-unused-parameter -O2 -ftree-vectorize -march=native -fno-math-errno
-DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY
-DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS
-DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DSERIALIZATION -DNDEBUG
-DUSEMPI -DMPICH_IGNORE_CXX_SEEK -Iexternal/include
-I/opt/site/easybuild/software/ScaLAPACK/2.0.2-gompi-2019b/include
-I/opt/site/easybuild/software/FFTW/3.3.8-gompi-2019b/include
-I/opt/site/easybuild/software/OpenBLAS/0.3.7-GCC-8.3.0/include
-I/opt/site/easybuild/software/OpenMPI/3.1.4-GCC-8.3.0/include
-I/opt/site/easybuild/software/hwloc/1.11.12-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/libpciaccess/0.14-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/libxml2/2.9.9-GCCcore-8.3.0/include/libxml2
-I/opt/site/easybuild/software/libxml2/2.9.9-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/XZ/5.2.4-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/numactl/2.0.12-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/binutils/2.32-GCCcore-8.3.0/include
-I/opt/site/easybuild/software/zlib/1.2.11-GCCcore-8.3.0/include
external/libxml2/nanoftp.c
scons: ***
[build/external/release/linux/3.10/64/x86/gcc/8.3/mpi-serialization/libxml2/HTMLparser.os]
Error 1
external/libxml2/list.c:676:1: error: conflicting types for 'xmlListWalk'
xmlListWalk(xmlListPtr l, xmlListWalker walker, const void *user) {
Is there any way to reset the include path so as not to have the easybuild
libxml2?
Note: I am using an older toolchain becase there are problems compiling rosetta
with newer compilers. I can compile Rosetta using the 2019b toolchain but not
through EasyBuild.
<https://www.njit.edu/> Glenn (Gedaliah) Wolosh, Ph.D.
Ass't Director Research Software and Cloud Computing
Acad & Research Computing Systems
[email protected] <mailto:[email protected]> • (973) 596-5437 <tel:(973) 596-5437>
A Top 100 National University
U.S. News & World Report
