Issue installing psi4 from source

1

Hi,

I need to install psi4 from source in linux via conda. I am following the instructions

git clone GitHub - psi4/psi4: Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python && cd psi4
conda create -n p4dev psi4-dev python=3.8 -c psi4/label/dev
conda activate p4dev
psi4-path-advisor --gcc
cd objdir && make -jgetconf _NPROCESSORS_ONLN

but in the very last step I get the following error

[ 95%] Built target cc
make[4]: *** [CMakeFiles/Makefile2:1379: src/psi4/libmints/CMakeFiles/l2intf.dir/all] Error 2
make[3]: *** [Makefile:136: all] Error 2
make[2]: *** [CMakeFiles/psi4-core.dir/build.make:86: psi4-core-prefix/src/psi4-core-stamp/psi4-core-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:10116: CMakeFiles/psi4-core.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

I would really appreciate if someone could help me solve this issue

Thanks

2

That isn’t an error message. Give us the complete terminal output.

3

The complete terminal output is as follows

– Install configuration: “Release”
– Install configuration: “Release”
[ 20%] Built target lapack_external
[ 20%] Built target hdf5_external
[ 30%] Performing build step for ‘psi4-core’
Consolidate compiler generated dependencies of target diis
Consolidate compiler generated dependencies of target cubeprop
Consolidate compiler generated dependencies of target filesystem
Consolidate compiler generated dependencies of target disp
Consolidate compiler generated dependencies of target functional
Consolidate compiler generated dependencies of target 3index
Consolidate compiler generated dependencies of target options
[ 1%] Generating version info
[ 1%] Building CXX object src/CMakeFiles/l2export.dir/export_mints.cc.o
Consolidate compiler generated dependencies of target iwl
Consolidate compiler generated dependencies of target moinfo
Consolidate compiler generated dependencies of target ciomr
Consolidate compiler generated dependencies of target plugin
Consolidate compiler generated dependencies of target l2intf
Consolidate compiler generated dependencies of target psi4util
Consolidate compiler generated dependencies of target qt
[ 2%] Built target disp
[ 2%] Built target filesystem
[ 3%] Built target cubeprop
Consolidate compiler generated dependencies of target fock
[ 3%] Built target diis
[ 4%] Built target functional
[ 5%] Built target options
Consolidate compiler generated dependencies of target psio
[ 5%] Built target 3index
Consolidate compiler generated dependencies of target sapt_solver
[ 5%] Built target plugin
Consolidate compiler generated dependencies of target ambit_interface
[ 6%] Built target moinfo
[ 7%] Built target iwl
Consolidate compiler generated dependencies of target adc
[ 9%] Built target ciomr
Consolidate compiler generated dependencies of target trans
[ 10%] Built target psi4util
Consolidate compiler generated dependencies of target cctransort
Consolidate compiler generated dependencies of target dfep2
[ 10%] Built target ambit_interface
Consolidate compiler generated dependencies of target dmrg
Consolidate compiler generated dependencies of target dfmp2
[ 10%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/dipole.cc.o
[ 12%] Built target qt
Consolidate compiler generated dependencies of target dlpno
[ 12%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/electricfield.cc.o
[ 12%] Built target dfep2
[ 14%] Built target fock
[ 15%] Built target adc
Consolidate compiler generated dependencies of target dpd
Consolidate compiler generated dependencies of target dct
[ 17%] Built target psio
[ 17%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/eribase.cc.o
[ 17%] Built target dmrg
Consolidate compiler generated dependencies of target detci
[ 17%] Built target dfmp2
[ 18%] Built target trans
[ 19%] Built target cctransort
Consolidate compiler generated dependencies of target fisapt
Consolidate compiler generated dependencies of target gdma_interface
[ 19%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/eri.cc.o
[ 19%] Built target dlpno
[ 19%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/integral.cc.o
Consolidate compiler generated dependencies of target fnocc
[ 19%] Built target gdma_interface
[ 21%] Built target sapt_solver
Consolidate compiler generated dependencies of target mrcc
[ 21%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/kinetic.cc.o
[ 21%] Built target fisapt
Consolidate compiler generated dependencies of target mcscf
Consolidate compiler generated dependencies of target sapt
[ 21%] Built target mrcc
[ 22%] Built target fnocc
[ 22%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/potentialint.cc.o
Consolidate compiler generated dependencies of target optking
[ 23%] Built target sapt
[ 26%] Built target dct
[ 29%] Built target detci
Consolidate compiler generated dependencies of target occ
[ 29%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/quadrupole.cc.o
[ 29%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/rel_potential.cc.o
[ 29%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/tracelessquadrupole.cc.o
Consolidate compiler generated dependencies of target scf_solver
Consolidate compiler generated dependencies of target psimrcc
[ 31%] Built target mcscf
Consolidate compiler generated dependencies of target dfocc
[ 31%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/3coverlap.cc.o
[ 40%] Built target dpd
[ 41%] Built target scf_solver
[ 41%] Building CXX object src/psi4/libmints/CMakeFiles/l2intf.dir/siminteri.cc.o
[ 44%] Built target optking
[ 44%] Building CXX object src/psi4/scfgrad/CMakeFiles/scfgrad.dir/jk_grad.cc.o
[ 44%] Building CXX object src/psi4/scfgrad/CMakeFiles/scfgrad.dir/response.cc.o
[ 48%] Built target occ
[ 48%] Building CXX object src/psi4/scfgrad/CMakeFiles/scfgrad.dir/scf_grad.cc.o
[ 54%] Built target psimrcc
[ 54%] Building CXX object src/psi4/scfgrad/CMakeFiles/scfgrad.dir/wrapper.cc.o
Consolidate compiler generated dependencies of target cc
[ 62%] Built target dfocc
[ 94%] Built target cc
Defining development snapshot version: 1.7a1.dev56+e765321 (computed)
1.7a1.dev56 {master} e765321 1.6.0.999 1.6 ← 1.7a1.dev56+e765321
[ 94%] Built target update_version
x86_64-conda-linux-gnu-g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
make[5]: *** [src/psi4/libmints/CMakeFiles/l2intf.dir/build.make:286: src/psi4/libmints/CMakeFiles/l2intf.dir/rel_potential.cc.o] Error 4
make[5]: *** Deleting file ‘src/psi4/libmints/CMakeFiles/l2intf.dir/rel_potential.cc.o’
make[5]: *** Waiting for unfinished jobs…
x86_64-conda-linux-gnu-g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
make[5]: *** [src/psi4/libmints/CMakeFiles/l2intf.dir/build.make:90: src/psi4/libmints/CMakeFiles/l2intf.dir/electricfield.cc.o] Error 4
make[5]: *** Deleting file ‘src/psi4/libmints/CMakeFiles/l2intf.dir/electricfield.cc.o’
x86_64-conda-linux-gnu-g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
make[5]: *** [src/psi4/libmints/CMakeFiles/l2intf.dir/build.make:118: src/psi4/libmints/CMakeFiles/l2intf.dir/eribase.cc.o] Error 4
make[5]: *** Deleting file ‘src/psi4/libmints/CMakeFiles/l2intf.dir/eribase.cc.o’
x86_64-conda-linux-gnu-g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
make[5]: *** [src/psi4/libmints/CMakeFiles/l2intf.dir/build.make:300: src/psi4/libmints/CMakeFiles/l2intf.dir/tracelessquadrupole.cc.o] Error 4
make[5]: *** Deleting file ‘src/psi4/libmints/CMakeFiles/l2intf.dir/tracelessquadrupole.cc.o’
x86_64-conda-linux-gnu-g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
make[5]: *** [src/psi4/libmints/CMakeFiles/l2intf.dir/build.make:146: src/psi4/libmints/CMakeFiles/l2intf.dir/integral.cc.o] Error 4
make[5]: *** Deleting file ‘src/psi4/libmints/CMakeFiles/l2intf.dir/integral.cc.o’
x86_64-conda-linux-gnu-g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
make[5]: *** [src/psi4/libmints/CMakeFiles/l2intf.dir/build.make:258: src/psi4/libmints/CMakeFiles/l2intf.dir/potentialint.cc.o] Error 4
make[5]: *** Deleting file ‘src/psi4/libmints/CMakeFiles/l2intf.dir/potentialint.cc.o’
[ 94%] Linking CXX static library libscfgrad.a
[ 94%] Built target scfgrad
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc: In function ‘void export_mints(pybind11::module&)’:
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:506:42: warning: ‘Full’ is deprecated: Using Matrix::SaveType::Full instead of Matrix::SaveType::SubBlocks is deprecated, and as soon as 1.5 it will stop working [-Wdeprecated-declarations]
.value(“Full”, Matrix::SaveType::Full)
^~~~
In file included from /home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/deriv.h:40:0,
from /home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:37:
/home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/matrix.h:290:21: note: declared here
enum SaveType { Full
^~~~
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:506:42: warning: ‘Full’ is deprecated: Using Matrix::SaveType::Full instead of Matrix::SaveType::SubBlocks is deprecated, and as soon as 1.5 it will stop working [-Wdeprecated-declarations]
.value(“Full”, Matrix::SaveType::Full)
^~~~
In file included from /home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/deriv.h:40:0,
from /home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:37:
/home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/matrix.h:290:21: note: declared here
enum SaveType { Full
^~~~
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:729:38: warning: ‘SCF’ is deprecated: DerivCalcType::SCF is planned for removal in 1.7, due to lack of use and being superseded by the scfgrad library. Contact developers if you need this ability. [-Wdeprecated-declarations]
.value(“SCF”, DerivCalcType::SCF, “SCF methods.”)
^~~
In file included from /home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:37:0:
/home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/deriv.h:58:5: note: declared here
SCF PSI_DEPRECATED(
^~~
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:729:38: warning: ‘SCF’ is deprecated: DerivCalcType::SCF is planned for removal in 1.7, due to lack of use and being superseded by the scfgrad library. Contact developers if you need this ability. [-Wdeprecated-declarations]
.value(“SCF”, DerivCalcType::SCF, “SCF methods.”)
^~~
In file included from /home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:37:0:
/home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/deriv.h:58:5: note: declared here
SCF PSI_DEPRECATED(
^~~
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:730:43: warning: ‘SCFandDF’ is deprecated: DerivCalcType::SCFandDF is planned for removal in 1.7, due to lack of use and being superseded by the compute_df method. Contact developers if you need this ability. [-Wdeprecated-declarations]
.value(“SCFandDF”, DerivCalcType::SCFandDF, “Correlated methods using DF (no reference contribution).”)
^~~~~~~~
In file included from /home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:37:0:
/home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/deriv.h:62:5: note: declared here
SCFandDF PSI_DEPRECATED(
^~~~~~~~
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:730:43: warning: ‘SCFandDF’ is deprecated: DerivCalcType::SCFandDF is planned for removal in 1.7, due to lack of use and being superseded by the compute_df method. Contact developers if you need this ability. [-Wdeprecated-declarations]
.value(“SCFandDF”, DerivCalcType::SCFandDF, “Correlated methods using DF (no reference contribution).”)
^~~~~~~~
In file included from /home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:37:0:
/home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/deriv.h:62:5: note: declared here
SCFandDF PSI_DEPRECATED(
^~~~~~~~
x86_64-conda-linux-gnu-g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
make[5]: *** [src/psi4/libmints/CMakeFiles/l2intf.dir/build.make:314: src/psi4/libmints/CMakeFiles/l2intf.dir/3coverlap.cc.o] Error 4
make[5]: *** Deleting file ‘src/psi4/libmints/CMakeFiles/l2intf.dir/3coverlap.cc.o’
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:1668:38: warning: ‘void psi::MoldenWriter::write(const string&, std::shared_ptrpsi::Matrix, std::shared_ptrpsi::Matrix, std::shared_ptrpsi::Vector, std::shared_ptrpsi::Vector, std::shared_ptrpsi::Vector, std::shared_ptrpsi::Vector, bool)’ is deprecated: Constructing an MoldenWriter and then calling write instead of using wfn.write_molden(name) is both buggy and deprecated, and as soon as 1.5 it will stop working [-Wdeprecated-declarations]
.def(“write”, &MoldenWriter::write, “Writes wavefunction information in molden format”, “filename”_a, “Ca”_a,
^~~~~
In file included from /home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:63:0:
/home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/writer.h:86:10: note: declared here
void write(const std::string &filename, std::shared_ptr Ca, std::shared_ptr Cb,
^~~~~
/home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:1673:35: warning: ‘void psi::NBOWriter::write(const string&)’ is deprecated: Constructing an NBOWriter and then calling write instead of using wfn.nbo_write(name) is both buggy and deprecated, and as soon as 1.5 it will stop working [-Wdeprecated-declarations]
.def(“write”, &NBOWriter::write, “Write the natural bond orbitals to a file”, “filename”_a);
^~~~~
In file included from /home/daniel/instalingpsi4/psi4/psi4/src/export_mints.cc:63:0:
/home/daniel/instalingpsi4/psi4/psi4/src/psi4/libmints/writer.h:118:10: note: declared here
void write(const std::string &filename);
^~~~~
[ 94%] Built target l2export
make[4]: *** [CMakeFiles/Makefile2:1379: src/psi4/libmints/CMakeFiles/l2intf.dir/all] Error 2
make[3]: *** [Makefile:136: all] Error 2
make[2]: *** [CMakeFiles/psi4-core.dir/build.make:86: psi4-core-prefix/src/psi4-core-stamp/psi4-core-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:10116: CMakeFiles/psi4-core.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

4

Argh, those “internal compiler error” sound like what were were seeing on continuous integration with the 7.5 conda gcc a few weeks ago. The errors were non-determininstic, not previously seen on non-CI systems, and cleared up mysteriously after two weeks.

Apart from psi4 needing to bump up its gcc pin, I don’t know quite how to address this. Do you happen to have gcc on your system? That is, outside the conda environment, if you gcc --version, what does it give you?

5

The output of gcc --version from outside of conda environment is

gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0

6

aparently if I remove -jgetconf _NPROCESSORS_ONLN the build works but when trying to import in python I get the following error

raceback (most recent call last):
File “/usr/lib/x86_64-linux-gnu/psi4/init.py”, line 55, in
from . import core
ImportError: cannot import name ‘core’ from partially initialized module ‘psi4’ (most likely due to a circular import) (/usr/lib/x86_64-linux-gnu/psi4/init.py)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “”, line 1, in
File “/usr/lib/x86_64-linux-gnu/psi4/init.py”, line 60, in
raise ImportError(“{0}”.format(err))
ImportError: cannot import name ‘core’ from partially initialized module ‘psi4’ (most likely due to a circular import) (/usr/lib/x86_64-linux-gnu/psi4/init.py)

7

oh I just realized that when conda deactivate I am able to import psi4 in python

8

Any chance you’ve got a different psi installation at /usr/lib/ from the source you’re compiling at /home/daniel/installingpsi4/? If the former was in in PATH or accessible to system Python, that could explain things.

From your <objdir>, execute stage/bin/psi4 --psiapi and then execute what it prints (adding stuff to envvars). Then see what which conda python psi4 and python -c "import psi4;print(psi4.__file__, psi4.__version__) says, please.

9

The output is the following

/home/daniel/anaconda3/bin/conda
/home/daniel/anaconda3/envs/p4dev/bin/python
/home/daniel/instalingpsi4/psi4/objdir/stage/bin/psi4

/home/daniel/instalingpsi4/psi4/objdir/stage/lib/psi4/init.py

An it works properly now

Thank you

1 Like