Trouble installing MDAnalysis
Carolyn Phillips
src/numtools/calc_distances.h:27:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 warning and 1 error generated.
error: command '/usr/bin/clang' failed with exit status 1
The problem is clearly that "clang" is being used and, as per this thread,
instead of the compiler gcc.
Any idea how to force pip to use gcc? I think that should solve the problem
Oliver Beckstein
I don't have an answer to your question but I am surprised that you even ran into this problem. In principle we detect during setup if the compiler supports OpenMP and only if this is the case we set -DPARALLEL. Because clang does not support OpenMP, PARALLEL should not have been set and the '#include <omp.h>' should never have been included.
I hope that someone else can answer the question how to make pip use gcc (maybe as easy as installing from source and setting [build] compiler=gcc in setup.cfg ... or something along those lines... I didn't look) but could you also show the output from the installation command, in particular a line like 'Attempting to autodetect OpenMP support... Compiler supports OpenMP' is of interest.
See also https://github.com/MDAnalysis/mdanalysis/issues/145
Best,
Oliver
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skype: orbeckst * orbe...@gmail.com
Carolyn Phillips
Collecting MDAnalysis
Downloading MDAnalysis-0.11.0.tar.gz (8.9MB)
100% |████████████████████████████████| 8.9MB 52kB/s
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.5.0 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from MDAnalysis)
Requirement already satisfied (use --upgrade to upgrade): biopython>=1.59 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from MDAnalysis)
Requirement already satisfied (use --upgrade to upgrade): networkx>=1.0 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from MDAnalysis)
Requirement already satisfied (use --upgrade to upgrade): GridDataFormats>=0.2.2 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from MDAnalysis)
Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.0 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from networkx>=1.0->MDAnalysis)
Requirement already satisfied (use --upgrade to upgrade): six in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from GridDataFormats>=0.2.2->MDAnalysis)
Installing collected packages: MDAnalysis
Running setup.py install for MDAnalysis
Complete output from command /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c "import setuptools, tokenize;__file__='/private/tmp/pip-build-mq68Zp/MDAnalysis/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-Vki164-record/install-record.txt --single-version-externally-managed --compile:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
running install
running build
running build_py
creating build
creating build/lib.macosx-10.10-x86_64-2.7
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis
copying MDAnalysis/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis
copying MDAnalysis/exceptions.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis
copying MDAnalysis/KDTree.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis
copying MDAnalysis/units.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis
copying MDAnalysis/version.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/helanal.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/hole.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/psa.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/rms.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/waterdynamics.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/x3dna.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/analysis/hbonds
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DLPoly.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DMS.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GMS.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/INPCRD.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MOL2.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRZ.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/core.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/libxdrfile2.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/statno.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/TRR.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/XTC.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/xdrfile
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/pdb
copying MDAnalysis/coordinates/pdb/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/pdb
copying MDAnalysis/coordinates/pdb/extensions.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/pdb
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/AtomGroup.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/distances.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/log.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/parallel.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/qcprot.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/Selection.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/Timeseries.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/topologyobjects.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/transformations.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/units.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/util.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/core
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/distances.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/log.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/mdamath.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/NeighborSearch.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/transformations.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/util.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib/parallel
copying MDAnalysis/lib/parallel/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib/parallel
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/ten2eleven.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/migration/fixes
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/jmol.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/selections
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/base.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DLPolyParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DMSParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GMSParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MOL2Parser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PrimitivePDBParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TPRParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/XYZParser.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/obj.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/setting.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/utils.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/topology/tpr
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/tests
creating build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/visualization
running build_ext
building 'coordinates._dcdmodule' extension
creating build/temp.macosx-10.10-x86_64-2.7
creating build/temp.macosx-10.10-x86_64-2.7/src
creating build/temp.macosx-10.10-x86_64-2.7/src/dcd
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -pipe -Os -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -Isrc/dcd/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/dcd/dcd.c -o build/temp.macosx-10.10-x86_64-2.7/src/dcd/dcd.o
In file included from src/dcd/dcd.c:22:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
In file included from src/dcd/dcd.c:24:
In file included from src/dcd/include/readdcd.h:25:
src/dcd/include/endianswap.h:32:13: warning: unused function 'swap2_unaligned' [-Wunused-function]
static void swap2_unaligned(void *v, long ndata) {
^
src/dcd/include/endianswap.h:96:13: warning: unused function 'swap2_aligned' [-Wunused-function]
static void swap2_aligned(void *v, long ndata) {
^
In file included from src/dcd/dcd.c:24:
In file included from src/dcd/include/readdcd.h:26:
src/dcd/include/fastio.h:351:12: warning: unused function 'fio_open' [-Wunused-function]
static int fio_open(const char *filename, int mode, fio_fd *fd) {
^
src/dcd/include/fastio.h:370:12: warning: unused function 'fio_fclose' [-Wunused-function]
static int fio_fclose(fio_fd fd) {
^
src/dcd/include/fastio.h:446:12: warning: unused function 'fio_read_int32' [-Wunused-function]
static int fio_read_int32(fio_fd fd, int *i) {
^
src/dcd/include/fastio.h:450:12: warning: unused function 'fio_write_str' [-Wunused-function]
static int fio_write_str(fio_fd fd, const char *str) {
^
In file included from src/dcd/dcd.c:24:
src/dcd/include/readdcd.h:626:12: warning: unused function 'jump_to_dcdstep' [-Wunused-function]
static int jump_to_dcdstep(fio_fd fd, int natoms, int nsets, int nfixed, int charmm, int header_size, int step) {
^
8 warnings generated.
/usr/bin/clang -bundle -undefined dynamic_lookup -L/opt/local/lib -Wl,-headerpad_max_install_names -L/opt/local/lib/db48 build/temp.macosx-10.10-x86_64-2.7/src/dcd/dcd.o -o build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/_dcdmodule.so
skipping 'src/dcd/dcdtimeseries.c' Cython extension (up-to-date)
building 'coordinates.dcdtimeseries' extension
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -pipe -Os -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -Isrc/dcd/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/dcd/dcdtimeseries.c -o build/temp.macosx-10.10-x86_64-2.7/src/dcd/dcdtimeseries.o
In file included from src/dcd/dcdtimeseries.c:254:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
In file included from src/dcd/dcdtimeseries.c:255:
In file included from src/dcd/include/readdcd.h:25:
src/dcd/include/endianswap.h:32:13: warning: unused function 'swap2_unaligned' [-Wunused-function]
static void swap2_unaligned(void *v, long ndata) {
^
src/dcd/include/endianswap.h:96:13: warning: unused function 'swap2_aligned' [-Wunused-function]
static void swap2_aligned(void *v, long ndata) {
^
In file included from src/dcd/dcdtimeseries.c:255:
In file included from src/dcd/include/readdcd.h:26:
src/dcd/include/fastio.h:351:12: warning: unused function 'fio_open' [-Wunused-function]
static int fio_open(const char *filename, int mode, fio_fd *fd) {
^
src/dcd/include/fastio.h:370:12: warning: unused function 'fio_fclose' [-Wunused-function]
static int fio_fclose(fio_fd fd) {
^
src/dcd/include/fastio.h:433:19: warning: unused function 'fio_ftell' [-Wunused-function]
static fio_size_t fio_ftell(fio_fd fd) {
^
src/dcd/include/fastio.h:446:12: warning: unused function 'fio_read_int32' [-Wunused-function]
static int fio_read_int32(fio_fd fd, int *i) {
^
src/dcd/include/fastio.h:450:12: warning: unused function 'fio_write_str' [-Wunused-function]
static int fio_write_str(fio_fd fd, const char *str) {
^
In file included from src/dcd/dcdtimeseries.c:255:
src/dcd/include/readdcd.h:169:12: warning: unused function 'read_dcdheader' [-Wunused-function]
static int read_dcdheader(fio_fd fd, int *N, int *NSET, int *ISTART,
^
src/dcd/include/readdcd.h:502:12: warning: unused function 'read_dcdstep' [-Wunused-function]
static int read_dcdstep(fio_fd fd, int N, float *X, float *Y, float *Z,
^
src/dcd/include/readdcd.h:758:13: warning: unused function 'close_dcd_read' [-Wunused-function]
static void close_dcd_read(int *indexes, float *fixedcoords) {
^
src/dcd/include/readdcd.h:690:12: warning: unused function 'write_dcdheader' [-Wunused-function]
static int write_dcdheader(fio_fd fd, const char *remarks, int N,
^
src/dcd/include/readdcd.h:653:12: warning: unused function 'write_dcdstep' [-Wunused-function]
static int write_dcdstep(fio_fd fd, int curframe, int curstep, int N,
^
src/dcd/dcdtimeseries.c:3935:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function]
static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
^
src/dcd/dcdtimeseries.c:3932:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]
static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
^
src/dcd/dcdtimeseries.c:325:29: warning: unused function '__Pyx_Py_UNICODE_strlen' [-Wunused-function]
static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
^
src/dcd/dcdtimeseries.c:3997:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function]
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
^
src/dcd/dcdtimeseries.c:4047:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function]
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
^
src/dcd/dcdtimeseries.c:4072:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function]
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
^
src/dcd/dcdtimeseries.c:2945:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function]
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
^
src/dcd/dcdtimeseries.c:3217:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function]
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
^
src/dcd/dcdtimeseries.c:3232:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function]
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
^
src/dcd/dcdtimeseries.c:3701:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
^
23 warnings generated.
/usr/bin/clang -bundle -undefined dynamic_lookup -L/opt/local/lib -Wl,-headerpad_max_install_names -L/opt/local/lib/db48 build/temp.macosx-10.10-x86_64-2.7/src/dcd/dcdtimeseries.o -o build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/coordinates/dcdtimeseries.so
skipping 'src/numtools/distances.c' Cython extension (up-to-date)
building 'lib._distances' extension
creating build/temp.macosx-10.10-x86_64-2.7/src/numtools
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -pipe -Os -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -Isrc/numtools -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/numtools/distances.c -o build/temp.macosx-10.10-x86_64-2.7/src/numtools/distances.o
In file included from src/numtools/distances.c:254:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
src/numtools/distances.c:19801:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]
static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
^
src/numtools/distances.c:329:29: warning: unused function '__Pyx_Py_UNICODE_strlen' [-Wunused-function]
static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
^
src/numtools/distances.c:19941:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function]
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
^
src/numtools/distances.c:17763:26: warning: unused function '__Pyx_GetBufferAndValidate' [-Wunused-function]
static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
^
src/numtools/distances.c:17797:27: warning: unused function '__Pyx_SafeReleaseBuffer' [-Wunused-function]
static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
^
src/numtools/distances.c:17870:1: warning: unused function '__pyx_add_acquisition_count_locked' [-Wunused-function]
__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
^
src/numtools/distances.c:17880:1: warning: unused function '__pyx_sub_acquisition_count_locked' [-Wunused-function]
__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
^
src/numtools/distances.c:18454:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function]
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
^
src/numtools/distances.c:18469:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function]
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
^
src/numtools/distances.c:19200:27: warning: function '__Pyx_PyInt_As_char' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) {
^
src/numtools/distances.c:19305:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
^
12 warnings generated.
/usr/bin/clang -bundle -undefined dynamic_lookup -L/opt/local/lib -Wl,-headerpad_max_install_names -L/opt/local/lib/db48 build/temp.macosx-10.10-x86_64-2.7/src/numtools/distances.o -lm -o build/lib.macosx-10.10-x86_64-2.7/MDAnalysis/lib/_distances.so
skipping 'src/numtools/distances_openmp.c' Cython extension (up-to-date)
building 'lib._distances_openmp' extension
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -pipe -Os -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DPARALLEL -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -Isrc/numtools -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/numtools/distances_openmp.c -o build/temp.macosx-10.10-x86_64-2.7/src/numtools/distances_openmp.o -fopenmp
In file included from src/numtools/distances_openmp.c:254:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
In file included from src/numtools/distances_openmp.c:256:
src/numtools/calc_distances.h:27:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 warning and 1 error generated.
error: command '/usr/bin/clang' failed with exit status 1
----------------------------------------
Command "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c "import setuptools, tokenize;__file__='/private/tmp/pip-build-mq68Zp/MDAnalysis/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-Vki164-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-build-mq68Zp/MDAnalysis
On Tuesday, September 29, 2015 at 7:28:02 PM UTC-5, Oliver Beckstein wrote:
Hi Carolyn,
I don't have an answer to your question but I am surprised that you even ran into this problem. In principle we detect during setup if the compiler supports OpenMP and only if this is the case we set -DPARALLEL. Because clang does not support OpenMP, PARALLEL should not have been set and the '#include <omp.h>' should never have been included.
I hope that someone else can answer the question how to make pip use gcc (maybe as easy as installing from source and setting [build] compiler=gcc in setup.cfg ... or something along those lines... I didn't look) but could you also show the output from the installation command, in particular a line like 'Attempting to autodetect OpenMP support... Compiler supports OpenMP' is of interest.
See also https://github.com/MDAnalysis/mdanalysis/issues/145
Best,
Oliver
On 29 Sep, 2015, at 17:07, Carolyn Phillips wrote:
> Hi,
> So I recently upgraded my operating system to OSX Yosemite 10.10.5 and found I needed to reinstall MDAnalysis.
>
> Using either easy_install or pip I get the following error
>
> src/numtools/calc_distances.h:27:10: fatal error: 'omp.h' file not found
>
> #include <omp.h>
>
> ^
>
> 1 warning and 1 error generated.
>
> error: command '/usr/bin/clang' failed with exit status 1
>
>
>
>
>
> The problem is clearly that "clang" is being used and, as per this thread,
>
> http://stackoverflow.com/questions/28546288/omp-h-not-found-os-x-yosemite-not-using-newest-gcc-version
>
>
>
> instead of the compiler gcc.
>
>
>
> Any idea how to force pip to use gcc? I think that should solve the problem
>
>
>
>
>
>
>
>
>
>
>
>
> --
> You received this message because you are subscribed to the Google Groups "MDnalysis discussion" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to mdnalysis-discussion+unsub...@googlegroups.com.
Oliver Beckstein
> Certainly. As you can see below, it thought it detected a compiler compatible with OpenMP
Until we have a fix, you could do the following: Get the tarball and in the sources in
package/setup.py
add a line to manually set `has_openmp = False`:
has_openmp, needs_gomp = detect_openmp()
# hack to manually disable OpenMP
has_openmp = needs_gomp = False
parallel_args = ['-fopenmp'] if has_openmp else []
parallel_libraries = ['gomp'] if needs_gomp else []
parallel_macros = [('PARALLEL', None)] if has_openmp else []
Then install with
python setup.py install
Can you open an issue at https://github.com/MDAnalysis/mdanalysis/issues/new , please?
Thanks,
Oliver
Carolyn Phillips
python
Python 2.7.10 (default, Aug 26 2015, 18:17:29)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import MDAnalysis
>>> MDAnalysis/lib/transformations.py:1811: UserWarning: failed to import module _transformations
warnings.warn("failed to import module " + module_name)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "MDAnalysis/__init__.py", line 151, in <module>
from .lib import log
File "MDAnalysis/lib/__init__.py", line 30, in <module>
from . import distances # distances relies on mdamath
File "MDAnalysis/lib/distances.py", line 40, in <module>
from ._distances import (calc_distance_array,
ImportError: No module named _distances
Carolyn Phillips
Max Linke
How did you try build MDAnalysis, did you install openmp and what python version are you using (the version that comes with OSX / conda / homebrew?
A common way to specify compiler is to set the environment variables CC and CXX.
CC=gcc pip install --upgrade --user MDAnalysis
should force pip to use gcc. But I haven't tested that yet.
best Max
Carolyn Phillips
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Max Linke
for the openmp libraries?
To get the executable name run
from distutils.ccompiler import new_compiler
cc = new_compiler()
print(cc.compiler[0])
As this will likely return something like 'cc' you should afterwards run in a shell
<compiler name> --version
This which compiler was chosen. I hope that helps us to find out what went wrong.
best Max
Max Linke
CC=<your gcc binary> CXX=<your g++ binary> pip install --user --upgrade MDAnalysis
this should force PIP/setuptools to use gcc.
I also found a gist with a shell wrapper to pip that does this automatically
https://gist.github.com/scw/9961407
Carolyn Phillips
>>> from distutils.ccompiler import new_compiler
>>> cc = new_compiler()
>>> print(cc.compiler[0])
cc
>>> exit()
-> cc --version
Apple LLVM version 7.0.0 (clang-700.0.72)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
--
Carolyn Phillips
creating build/temp.macosx-10.10-x86_64-2.7/src/dcd
gcc -fno-strict-aliasing -fno-common -dynamic -pipe -Os -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include -Isrc/dcd/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/dcd/dcd.c -o build/temp.macosx-10.10-x86_64-2.7/src/dcd/dcd.o
src/dcd/dcd.c:1:0: error: unknown value ‘10.10’ of -mmacosx-version-min
Full output below
littleminion:Renewal2015-> CC=gcc CXX=g++ pip install --user --upgrade MDAnalysis
Collecting MDAnalysis
Using cached MDAnalysis-0.11.0.tar.gz
Requirement already up-to-date: numpy>=1.5.0 in /Users/phillicl/Library/Python/2.7/lib/python/site-packages (from MDAnalysis)
Requirement already up-to-date: biopython>=1.59 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from MDAnalysis)
Requirement already up-to-date: networkx>=1.0 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from MDAnalysis)
Requirement already up-to-date: GridDataFormats>=0.2.2 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from MDAnalysis)
Requirement already up-to-date: decorator>=3.4.0 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from networkx>=1.0->MDAnalysis)
Requirement already up-to-date: six in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from GridDataFormats>=0.2.2->MDAnalysis)
Building wheels for collected packages: MDAnalysis
Running setup.py bdist_wheel for MDAnalysis
Complete output from command /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c "import setuptools;__file__='/private/var/folders/l8/lk2mg_td0k5fzy__wfg4tvtr0000gp/T/pip-build-pn4tH1/MDAnalysis/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /var/folders/l8/lk2mg_td0k5fzy__wfg4tvtr0000gp/T/tmpX81JZupip-wheel-:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
running bdist_wheel
gcc -fno-strict-aliasing -fno-common -dynamic -pipe -Os -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include -Isrc/dcd/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/dcd/dcd.c -o build/temp.macosx-10.10-x86_64-2.7/src/dcd/dcd.o
src/dcd/dcd.c:1:0: error: unknown value ‘10.10’ of -mmacosx-version-min
/* -*- Mode: C; tab-width: 4; indent-tabs-mode:nil; -*- */
^
In file included from /Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
from /Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from src/dcd/dcd.c:22:
/Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
src/dcd/dcd.c: In function ‘__reset_dcd_read’:
src/dcd/dcd.c:892:7: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]
int rc;
^
In file included from src/dcd/include/readdcd.h:25:0,
from src/dcd/dcd.c:24:
src/dcd/dcd.c: At top level:
src/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]
static void swap2_unaligned(void *v, long ndata) {
^
src/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]
static void swap2_aligned(void *v, long ndata) {
^
In file included from src/dcd/include/readdcd.h:26:0,
from src/dcd/dcd.c:24:
src/dcd/include/fastio.h:351:12: warning: ‘fio_open’ defined but not used [-Wunused-function]
static int fio_open(const char *filename, int mode, fio_fd *fd) {
^
src/dcd/include/fastio.h:370:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function]
static int fio_fclose(fio_fd fd) {
^
src/dcd/include/fastio.h:446:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
static int fio_read_int32(fio_fd fd, int *i) {
^
src/dcd/include/fastio.h:450:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
static int fio_write_str(fio_fd fd, const char *str) {
^
In file included from src/dcd/dcd.c:24:0:
src/dcd/include/readdcd.h:626:12: warning: ‘jump_to_dcdstep’ defined but not used [-Wunused-function]
static int jump_to_dcdstep(fio_fd fd, int natoms, int nsets, int nfixed, int charmm, int header_size, int step) {
^
error: command 'gcc' failed with exit status 1
----------------------------------------
Failed building wheel for MDAnalysis
Failed to build MDAnalysis
Installing collected packages: MDAnalysis
Running setup.py install for MDAnalysis
Complete output from command /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c "import setuptools, tokenize;__file__='/private/var/folders/l8/lk2mg_td0k5fzy__wfg4tvtr0000gp/T/pip-build-pn4tH1/MDAnalysis/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/l8/lk2mg_td0k5fzy__wfg4tvtr0000gp/T/pip-RgPIte-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
running install
running build
running build_py
running build_ext
building 'coordinates._dcdmodule' extension
gcc -fno-strict-aliasing -fno-common -dynamic -pipe -Os -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include -Isrc/dcd/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/dcd/dcd.c -o build/temp.macosx-10.10-x86_64-2.7/src/dcd/dcd.o
src/dcd/dcd.c:1:0: error: unknown value ‘10.10’ of -mmacosx-version-min
/* -*- Mode: C; tab-width: 4; indent-tabs-mode:nil; -*- */
^
In file included from /Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
from /Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from src/dcd/dcd.c:22:
/Users/phillicl/Library/Python/2.7/lib/python/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
src/dcd/dcd.c: In function ‘__reset_dcd_read’:
src/dcd/dcd.c:892:7: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]
int rc;
^
In file included from src/dcd/include/readdcd.h:25:0,
from src/dcd/dcd.c:24:
src/dcd/dcd.c: At top level:
src/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]
static void swap2_unaligned(void *v, long ndata) {
^
src/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]
static void swap2_aligned(void *v, long ndata) {
^
In file included from src/dcd/include/readdcd.h:26:0,
from src/dcd/dcd.c:24:
src/dcd/include/fastio.h:351:12: warning: ‘fio_open’ defined but not used [-Wunused-function]
static int fio_open(const char *filename, int mode, fio_fd *fd) {
^
src/dcd/include/fastio.h:370:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function]
static int fio_fclose(fio_fd fd) {
^
src/dcd/include/fastio.h:446:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
static int fio_read_int32(fio_fd fd, int *i) {
^
src/dcd/include/fastio.h:450:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
static int fio_write_str(fio_fd fd, const char *str) {
^
In file included from src/dcd/dcd.c:24:0:
src/dcd/include/readdcd.h:626:12: warning: ‘jump_to_dcdstep’ defined but not used [-Wunused-function]
static int jump_to_dcdstep(fio_fd fd, int natoms, int nsets, int nfixed, int charmm, int header_size, int step) {
^
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c "import setuptools, tokenize;__file__='/private/var/folders/l8/lk2mg_td0k5fzy__wfg4tvtr0000gp/T/pip-build-pn4tH1/MDAnalysis/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/l8/lk2mg_td0k5fzy__wfg4tvtr0000gp/T/pip-RgPIte-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /private/var/folders/l8/lk2mg_td0k5fzy__wfg4tvtr0000gp/T/pip-build-pn4tH1/MDAnalysis
littleminion:Renewal2015-> g++ --version
g++: warning: couldn’t understand kern.osversion ‘14.5.0
g++ (GCC) 4.9.0 20130929 (experimental)
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Max Linke
The error you are seeing now is related to building the object file. Apparently your compiler doesn't understand it.
https://en.wikipedia.org/wiki/Mach-O#Minimum_Mac_OS_X_version
I found some information on google about problems with GCC and osx 10.10 but concret about your error nothing about that.
I'll see if I can make a small dummy package to test the compilation of cython generated code with your gcc.
Another thing is that I suspect we have an error in detecting if a compiler can run openmp. Could you be so nice an play around in the
source code? In the detect_openmp function it would be nice to print our the detected compiler like in the previous code and at what
stage that function thinks it has detected openmp.
Carolyn Phillips
gcc --version
gcc: warning: couldn’t understand kern.osversion ‘14.5.0
gcc (GCC) 4.9.0 20130929 (experimental)
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
So I did some printing out inside def detect_openmp():
What I see is that the compiler is "cc"
hasopenmp returns "False"
then, after these lines
>compiler.add_library('gomp')
>hasopenmp = hasfunction(compiler, 'omp_get_num_threads()')
now hasopenmp returns "True"
I see that https://gcc.gnu.org/projects/gomp/ is the openmp library for gcc.
However, the compiler is still cc. (e.g. clang)
Perhaps this is the problem?
Max Linke
I posted a possible solution on github you can see if that gets things working for you.
best Max
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