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libAtoms / QUIP

libAtoms/QUIP molecular dynamics framework: https://libatoms.github.io
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undefined symbol: dgemm_ #609

Open yg2831 opened 1 year ago

yg2831 commented 1 year ago

I've got the error code during "make test" ImportError: /home/kyg/.local/lib/python3.10/site-packages/quippy/_quippy.cpython-310-x8664-linux-gnu.so: undefined symbol: dgemm

I searched and figured out my MATH_LINKOPTS can be a key to solve this problem, but I don't know how to fix it my setting is like this MATH_LINKOPTS= -llapack.so -lblas.so -L/usr/lib/x86_64-linux-gnu/libblas.so -L/usr/lib/x86_64-linux-gnu/liblapack.so I tried -llapck -lblas -llapack.so -lblas.so

and I appended "export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu" at my .bashrc

Plz help me

bernstei commented 1 year ago

Th "-L" options should only include the directory that the libraries are in. The "-l" (lower case ell) options should include the library name without the leading "lib" or the trailing ".a" or ".so" or anything else, so definitely "-llapack -lblas", assuming that's what those libraries are actually named on your system.

jameskermode commented 1 year ago

Also often the -L/directory option needs to come BEFORE the -llibrary options.

yg2831 commented 1 year ago

MATH_LINKOPTS= -L/usr/lib/x86_64-linux-gnu -llapack -lblas

this is my final result. -L option comes before -llbrary option and -L includes only directory, -l includes only library name. but it doesn't work yet :(

it's my .bashrc info export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu

and I checked nm $ nm -D /usr/lib/x8664-linux-gnu/liblapack.so | grep 'dgemm' U dgemm_ $ nm -D /usr/lib/x8664-linux-gnu/libblas.so | grep 'dgemm' 000000000004f360 T dgemm_

what can I do another trier ? I appreciate for your help

bernstei commented 1 year ago

First, make sure that you cleaned up and recompiled after you changed those options. Can you upload the full output of the compilation and python install?

Also, what's the output of ldd /home/kyg/.local/lib/python3.10/site-packages/quippy/quippy.cpython-310-x86_64-linux-gnu.so ?

yg2831 commented 1 year ago

Sorry for my late answer. About the ldd ~~ there's no quippy.cpython~~ but is _quippy.cpython~~

and here's my compile log

kyg@kyg-H510:~/QUIP$ make test Using QUIP_ARCH=linux_x86_64_gfortran, MODULES=libAtoms Potentials Utils, QUIP_ROOT=/home/kyg/QUIP

Making libAtoms

rm -f /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile cp /home/kyg/QUIP/src/libAtoms/Makefile /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C /home/kyg/QUIP/build/linux_x86_64_gfortran QUIP_ROOT=/home/kyg/QUIP VPATH=/home/kyg/QUIP/src/libAtoms -I/home/kyg/QUIP -I/home/kyg/QUIP/arch make[1]: Entering directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' make[1]: Nothing to be done for 'default'. make[1]: Leaving directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' rm /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile

Making Potentials

rm -f /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile cp /home/kyg/QUIP/src/Potentials/Makefile /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C /home/kyg/QUIP/build/linux_x86_64_gfortran QUIP_ROOT=/home/kyg/QUIP VPATH=/home/kyg/QUIP/src/Potentials -I/home/kyg/QUIP -I/home/kyg/QUIP/arch make[1]: Entering directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' make[1]: Nothing to be done for 'default'. make[1]: Leaving directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' rm /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile

Making Utils

rm -f /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile cp /home/kyg/QUIP/src/Utils/Makefile /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C /home/kyg/QUIP/build/linux_x86_64_gfortran QUIP_ROOT=/home/kyg/QUIP VPATH=/home/kyg/QUIP/src/Utils -I/home/kyg/QUIP -I/home/kyg/QUIP/arch make[1]: Entering directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' rm /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile LIBQUIP_OBJS="ts_params.o transition_state.o elasticity.o phonons.o restraints_constraints_xml.o crackparams.o cracktools.o real_space_covariance.o structure_analysis_traj_routines.o RS_SparseMatrix.o QUIP_Common.o Functions.o Ewald.o Multipole_Interactions.o Partridge_Schwenke_Dipole.o IPEwald.o Yukawa.o Multipoles.o IPModel_GAP.o IPModel_LJ.o IPModel_Morse.o IPModel_FC.o IPModel_SW.o IPModel_Tersoff.o IPModel_EAM_Ercolessi_Adams.o IPModel_Brenner.o IPModel_FS.o IPModel_BOP.o IPModel_FB.o IPModel_Si_MEAM.o IPModel_Brenner_Screened.o IPModel_Brenner_2002.o IPModel_TS.o IPModel_Glue.o IPModel_PartridgeSchwenke.o IPModel_Einstein.o IPModel_Coulomb.o IPModel_Sutton_Chen.o IPModel_FX.o IPModel_HFdimer.o IPModel_BornMayer.o IPModel_Custom.o IPModel_ConfiningMonomer.o IPModel_SW_VP.o IPModel_WaterDimer_Gillan.o IPModel_WaterTrimer_Gillan.o IPModel_Tether.o IPModel_LMTO_TBE.o IPModel_Multipoles.o IPModel_FC4.o IPModel_Spring.o IPModel_DispTS.o IPModel_SCME.o IPModel_MTP.o IPModel_MBD.o IPModel_ZBL.o IPModel_LinearSOAP.o IPModel_TTM_nF.o IPModel_CH4.o IPModel_vdW.o IPModel_RS.o IPModel_Template.o IP.o FilePot.o CallbackPot.o SocketPot.o Potential_simple.o AdjustablePotential.o Potential.o ElectrostaticEmbed.o quip_unified_wrapper.o quip_lammps_wrapper.o Potential_Precon_Minim.o lbfgs.o error.o kind_module.o System.o LinkedList.o ExtendableStr.o MPI_context.o Units.o linearalgebra.o Quaternions.o statistics.o Dictionary.o Table.o ParamReader.o PeriodicTable.o minimization.o Atoms_types.o Connection.o DomainDecomposition.o Atoms.o RigidBody.o Group.o angular_functions.o steinhardt_nelson_qw.o gamma_functions.o Constraints.o Thermostat.o Barostat.o DynamicalSystem.o Spline.o Sparse.o CInOutput.o clusters.o Structures.o frametools.o nye_tensor.o Topology.o Atoms_ll.o ringstat.o histogram1d.o find_surface_atoms.o k_means_clustering.o SocketTools.o partition.o libAtoms.o libAtoms_misc_utils.o libAtoms_utils_no_module.o f90wrap_stub.o ScaLAPACK.o Matrix.o task_manager.o md5.o cutil.o netcdf.o xyz.o sockets.o m_sax_types.o m_sax_tokenizer.o m_sax_reader.o m_sax_parser.o m_sax_operate.o m_sax_xml_source.o FoX_sax.o m_wxml_escape.o m_wxml_core.o m_wxml_overloads.o FoX_wxml.o FoX_utils.o fox_m_utils_mtprng.o fox_m_utils_uuid.o fox_m_utils_uri.o m_common_attrs.o m_common_buffer.o m_common_charset.o m_common_namespaces.o m_common_error.o m_common_elstack.o m_common_io.o FoX_common.o m_common_namecheck.o m_common_entities.o m_common_notations.o m_common_element.o m_common_struct.o m_common_entity_expand.o m_common_content_model.o fox_m_fsys_abort_flush.o fox_m_fsys_array_str.o fox_m_fsys_format.o fox_m_fsys_parse_input.o fox_m_fsys_count_parse_input.o fox_m_fsys_string.o fox_m_fsys_string_list.o fox_m_fsys_realtypes.o fox_m_fsys_varstr.o" && \ cd /home/kyg/QUIP/build/linux_x86_64_gfortran && for i in /home/kyg/QUIP/src/fox/objs.linux_x86_64_gfortran/lib/libFoX_sax.a /home/kyg/QUIP/src/fox/objs.linux_x86_64_gfortran/lib/libFoX_wxml.a /home/kyg/QUIP/src/fox/objs.linux_x86_64_gfortran/lib/libFoX_utils.a /home/kyg/QUIP/src/fox/objs.linux_x86_64_gfortran/lib/libFoX_common.a /home/kyg/QUIP/src/fox/objs.linux_x86_64_gfortran/lib/libFoX_fsys.a; do ar -x $i; done && ar -rcs libquip.a $LIBQUIP_OBJS cd /home/kyg/QUIP/build/linux_x86_64_gfortran && cp libquip.a libquip_nostub.a && ar d libquip_nostub.a f90wrap_stub.o

Making Programs

rm -f /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile cp /home/kyg/QUIP/src/Programs/Makefile /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C /home/kyg/QUIP/build/linux_x86_64_gfortran QUIP_ROOT=/home/kyg/QUIP VPATH=/home/kyg/QUIP/src/Programs -I/home/kyg/QUIP -I/home/kyg/QUIP/arch make[1]: Entering directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' make[1]: Nothing to be done for 'default'. make[1]: Leaving directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' rm /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile

Making FilePot_drivers

rm -f /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile cp /home/kyg/QUIP/src/FilePot_drivers/Makefile /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C /home/kyg/QUIP/build/linux_x86_64_gfortran QUIP_ROOT=/home/kyg/QUIP VPATH=/home/kyg/QUIP/src/FilePot_drivers -I/home/kyg/QUIP -I/home/kyg/QUIP/arch make[1]: Entering directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' make[1]: Nothing to be done for 'default'. make[1]: Leaving directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' rm /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile

Making Structure_processors

rm -f /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile cp /home/kyg/QUIP/src/Structure_processors/Makefile /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C /home/kyg/QUIP/build/linux_x86_64_gfortran QUIP_ROOT=/home/kyg/QUIP VPATH=/home/kyg/QUIP/src/Structure_processors -I/home/kyg/QUIP -I/home/kyg/QUIP/arch make[1]: Entering directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' make[1]: Nothing to be done for 'default'. make[1]: Leaving directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' rm /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile

Making quippy

rm -f /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile cp /home/kyg/QUIP/quippy/Makefile /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C /home/kyg/QUIP/build/linux_x86_64_gfortran QUIP_ROOT=/home/kyg/QUIP -I/home/kyg/QUIP -I/home/kyg/QUIP/arch build make[1]: Entering directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' make[1]: -c: No such file or directory make[1]: -c: No such file or directory make[1]: -c: No such file or directory make[1]: -c: No such file or directory make[1]: -c: No such file or directory /usr/bin/pip install "f90wrap>=0.2.6" Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: f90wrap>=0.2.6 in /home/kyg/.local/lib/python3.10/site-packages (0.2.13) Requirement already satisfied: numpy>=1.13 in /home/kyg/.local/lib/python3.10/site-packages (from f90wrap>=0.2.6) (1.25.1) DEPRECATION: distro-info 1.1build1 has a non-standard version number. pip 23.3 will enforce this behaviour change. A possible replacement is to upgrade to a newer version of distro-info or contact the author to suggest that they release a version with a conforming version number. Discussion can be found at https://github.com/pypa/pip/issues/12063 /home/kyg/QUIP/bin/gitversion --hash-only > VERSION cp -r ../../quippy/quippy/*.py quippy make[1]: Leaving directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' rm /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile

Installing quippy

rm -f /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile cp /home/kyg/QUIP/quippy/Makefile /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C /home/kyg/QUIP/build/linux_x86_64_gfortran QUIP_ROOT=/home/kyg/QUIP -I/home/kyg/QUIP -I/home/kyg/QUIP/arch install make[1]: Entering directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' make[1]: -c: No such file or directory make[1]: -c: No such file or directory make[1]: -c: No such file or directory make[1]: -c: No such file or directory make[1]: -c: No such file or directory /usr/bin/pip install "f90wrap>=0.2.6" Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: f90wrap>=0.2.6 in /home/kyg/.local/lib/python3.10/site-packages (0.2.13) Requirement already satisfied: numpy>=1.13 in /home/kyg/.local/lib/python3.10/site-packages (from f90wrap>=0.2.6) (1.25.1) DEPRECATION: distro-info 1.1build1 has a non-standard version number. pip 23.3 will enforce this behaviour change. A possible replacement is to upgrade to a newer version of distro-info or contact the author to suggest that they release a version with a conforming version number. Discussion can be found at https://github.com/pypa/pip/issues/12063 /home/kyg/QUIP/bin/gitversion --hash-only > VERSION cp -r ../../quippy/quippy/*.py quippy cp ../../README.md ../../quippy/setup.py . cp quip md vasp_driver quippy/ /usr/bin/pip install . Defaulting to user installation because normal site-packages is not writeable Processing /home/kyg/QUIP/build/linux_x86_64_gfortran Preparing metadata (setup.py) ... done Requirement already satisfied: ase>=3.17.0 in /home/kyg/.local/lib/python3.10/site-packages (from quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (3.22.1) Requirement already satisfied: f90wrap>=0.2.6 in /home/kyg/.local/lib/python3.10/site-packages (from quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (0.2.13) Requirement already satisfied: numpy>=1.13 in /home/kyg/.local/lib/python3.10/site-packages (from quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (1.25.1) Requirement already satisfied: matplotlib>=3.1.0 in /home/kyg/.local/lib/python3.10/site-packages (from ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (3.7.2) Requirement already satisfied: scipy>=1.1.0 in /home/kyg/.local/lib/python3.10/site-packages (from ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (1.11.1) Requirement already satisfied: contourpy>=1.0.1 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (1.1.0) Requirement already satisfied: cycler>=0.10 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (4.41.1) Requirement already satisfied: kiwisolver>=1.0.1 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (1.4.4) Requirement already satisfied: packaging>=20.0 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (23.1) Requirement already satisfied: pillow>=6.2.0 in /usr/lib/python3/dist-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (9.0.1) Requirement already satisfied: pyparsing<3.1,>=2.3.1 in /usr/lib/python3/dist-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (2.4.7) Requirement already satisfied: python-dateutil>=2.7 in /usr/lib/python3/dist-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase==0.9+git0.9.14.2.gb0e43ebef.dirty) (2.8.1) Building wheels for collected packages: quippy-ase Building wheel for quippy-ase (setup.py) ... done Created wheel for quippy-ase: filename=quippy_ase-0.9+git0.9.14.2.gb0e43ebef.dirty-cp310-cp310-linux_x86_64.whl size=8253738 sha256=99c27fca9063f6826ff11c95c3605946c1e67f67fc7353ba1a437897c6220d9a Stored in directory: /tmp/pip-ephem-wheel-cache-luehe47z/wheels/d6/db/9a/35209a9dbf39967be8ab5c6e076d7f2daca271950fc0c586d8 Successfully built quippy-ase DEPRECATION: distro-info 1.1build1 has a non-standard version number. pip 23.3 will enforce this behaviour change. A possible replacement is to upgrade to a newer version of distro-info or contact the author to suggest that they release a version with a conforming version number. Discussion can be found at https://github.com/pypa/pip/issues/12063 Installing collected packages: quippy-ase Attempting uninstall: quippy-ase Found existing installation: quippy-ase 0.9+git0.9.14.2.gb0e43ebef.dirty Uninstalling quippy-ase-0.9+git0.9.14.2.gb0e43ebef.dirty: Successfully uninstalled quippy-ase-0.9+git0.9.14.2.gb0e43ebef.dirty WARNING: The scripts md, quip, quip-config and vasp_driver are installed in '/home/kyg/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed quippy-ase-0.9+git0.9.14.2.gb0e43ebef.dirty make[1]: Leaving directory '/home/kyg/QUIP/build/linux_x86_64_gfortran' rm /home/kyg/QUIP/build/linux_x86_64_gfortran/Makefile make -C tests -I/home/kyg/QUIP -I/home/kyg/QUIP/arch -I/home/kyg/QUIP/build/linux_x86_64_gfortran make[1]: Entering directory '/home/kyg/QUIP/tests' HAVE_GAP=0 HAVE_SCALAPACK=0 QUIP_ARCH=linux_x86_64_gfortran python3 run_all.py -v /home/kyg/QUIP/tests/run_all.py:22: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.util import get_platform /home/kyg/QUIP/tests/run_all.py:23: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead from distutils.sysconfig import get_python_version Traceback (most recent call last): File "/home/kyg/QUIP/tests/run_all.py", line 25, in import quippy File "/home/kyg/.local/lib/python3.10/site-packages/quippy/init.py", line 2, in import quippy._quippy ImportError: /home/kyg/.local/lib/python3.10/site-packages/quippy/_quippy.cpython-310-x8664-linux-gnu.so: undefined symbol: dgemm make[1]: [Makefile:31: all] Error 1 make[1]: Leaving directory '/home/kyg/QUIP/tests' make: [Makefile:296: test] Error 2

bernstei commented 1 year ago

there's no quippy.cpython~~ but is _quippy.cpython~~

Umm - this line

ImportError: /home/kyg/.local/lib/python3.10/site-packages/quippy/quippy.cpython-310-x86_64-linux-gnu.so: undefined symbol: dgemm

lists a file. Does that file actually not exist?

yg2831 commented 1 year ago

kyg@kyg-H510:~/.local/lib/python3.10/site-packages/quippy$ ls atoms_module.py dynamicalsystem_module.py nye_tensor.py _quippy.cpython-310-x86_64 atoms_types_module.py dynamicalsystem.py potential_module.py _quippy.cpython-310-x86_64-linux-gnu.so cli.py gap_tools.py potential.py system_module.py convert.py init.py potential_simple_module.py test.py descriptors.py md pycache vasp_driver dictionary_module.py nye_tensor_module.py quip

I changed _quippy.cpython-310-x86_64-linux-gnu.so > quippy.cpython-310-x86_64-linux-gnu.so by ImportError: /home/kyg/.local/lib/python3.10/site-packages/quippy/quippy.cpython-310-x86_64-linux-gnu.so: undefined symbol: dgemm but during "make test" process "make install" get start so another _quippy.cpython-310-x86_64-linux-gnu.so is produced and error is same :(

bernstei commented 1 year ago

First, please use code blocks (three back quotes) when pasting command output, otherwise the spacing gets messed up.

Second, don't blindly rename files in automatically installed directories - that's essentially never a good idea.

I'm not sure why the filename has an extra underscore, but please paste the output of ldd on the file with the closest name, e.g.

ldd /home/kyg/.local/lib/python3.10/site-packages/quippy/*.so
yg2831 commented 1 year ago

Thx for ur advice.

ldd /home/kyg/.local/lib/python3.10/site-packages/quippy/*.so output -> linux-vdso.so.1 (0x00007ffca19ba000) libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007f0cfaa00000) libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f0cfad19000) libmvec.so.1 => /usr/lib/x86_64-linux-gnu/libmvec.so.1 (0x00007f0cfa903000) libgcc_s.so.1 => /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f0d0110a000) libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f0cfa600000) libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f0d010c0000) /lib64/ld-linux-x86-64.so.2 (0x00007f0d0112c000)

bernstei commented 1 year ago

I'm at a loss. The filename starting with underscore is true on my installation too, so I guess that's normal. Do you get the error if you do

python -c "import quippy"

(or python3 or whatever the right python 3.10 executable is named)

Also, is there a specific reason you're not just using the pip installation?

yg2831 commented 1 year ago

kyg@kyg-H510:~$ python3 -c "import quippy" Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/kyg/.local/lib/python3.10/site-packages/quippy/__init__.py", line 2, in <module> import quippy._quippy ImportError: /home/kyg/.local/lib/python3.10/site-packages/quippy/_quippy.cpython-310-x86_64-linux-gnu.so: undefined symbol: dgemm_

i don't understand I'm not using the pip installation, Pip installation for what??

bernstei commented 1 year ago

Pip installation for what??

For quip/quippy - python3 -m pip install quippy-ase. I've been assuming, given that your make test is failing during the python part, that what you want is the python interface, although the python installation also includes some of the fortran executables, including gap_fit, quip, md, and maybe a couple others.

yg2831 commented 1 year ago

u mean, i have to proceed python3 -m pip install quippy-ase?

but i think i already got this kyg@kyg-H510:~/QUIP/build/linux_x86_64_gfortran$ python3 -m pip install quippy-ase

Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: quippy-ase in /home/kyg/.local/lib/python3.10/site-packages (0.9+git0.9.14.2.gb0e43ebef.dirty) Requirement already satisfied: ase>=3.17.0 in /home/kyg/.local/lib/python3.10/site-packages (from quippy-ase) (3.22.1) Requirement already satisfied: f90wrap>=0.2.6 in /home/kyg/.local/lib/python3.10/site-packages (from quippy-ase) (0.2.13) Requirement already satisfied: numpy>=1.13 in /home/kyg/.local/lib/python3.10/site-packages (from quippy-ase) (1.25.1) Requirement already satisfied: matplotlib>=3.1.0 in /home/kyg/.local/lib/python3.10/site-packages (from ase>=3.17.0->quippy-ase) (3.7.2) Requirement already satisfied: scipy>=1.1.0 in /home/kyg/.local/lib/python3.10/site-packages (from ase>=3.17.0->quippy-ase) (1.11.1) Requirement already satisfied: contourpy>=1.0.1 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase) (1.1.0) Requirement already satisfied: cycler>=0.10 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase) (4.41.1) Requirement already satisfied: kiwisolver>=1.0.1 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase) (1.4.4) Requirement already satisfied: packaging>=20.0 in /home/kyg/.local/lib/python3.10/site-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase) (23.1) Requirement already satisfied: pillow>=6.2.0 in /usr/lib/python3/dist-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase) (9.0.1) Requirement already satisfied: pyparsing<3.1,>=2.3.1 in /usr/lib/python3/dist-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase) (2.4.7) Requirement already satisfied: python-dateutil>=2.7 in /usr/lib/python3/dist-packages (from matplotlib>=3.1.0->ase>=3.17.0->quippy-ase) (2.8.1) DEPRECATION: distro-info 1.1build1 has a non-standard version number. pip 23.3 will enforce this behaviour change. A possible replacement is to upgrade to a newer version of distro-info or contact the author to suggest that they release a version with a conforming version number. Discussion can be found at https://github.com/pypa/pip/issues/12063