Can you show us the actual easyconfig? Is there a way to disable building the internal libxml2? I see you can use extras=hdf5 to add extras so maybe there is another option to turn them off?
On Thu, 3 Feb 2022 at 19:44, Glenn (Gedaliah) Wolosh <[email protected]> wrote: > 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. > > > > > [image: NJIT logo] <https://www.njit.edu/> *Glenn (Gedaliah) Wolosh, > Ph.D.* > Ass't Director Research Software and Cloud Computing > Acad & Research Computing Systems > [email protected] • (973) 596-5437 <(973)%20596-5437> > > A Top 100 National University > *U.S. News & World Report* > > > > > >
