Installation, testing and configuring psi4

I have been trying to setup psi4 on my personal linux machine by following instructions given at Install v1.4+ | Installs

# download via button above  -OR-  following line
 curl "http://vergil.chemistry.gatech.edu/psicode-download/Psi4conda-1.4-py38-Linux-x86_64.sh" -o Psi4conda-1.4-py38-Linux-x86_64.sh --keepalive-time 2
 bash Psi4conda-1.4-py38-Linux-x86_64.sh -b -p $HOME/psi4conda
  echo $'. $HOME/psi4conda/etc/profile.d/conda.sh\nconda activate' >> ~/.bashrc
  echo "source $HOME/psi4conda/etc/profile.d/conda.csh\nconda activate" >> ~/.tcshrc
# log out, log back in so conda and psi4 in path
 psi4 --test

When I run the tests, some of them seem to fail and have issues with certain packages.

Here is the warning and test summary

================================================ warnings summary =================================================
psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py: 31 warnings
Using `psi4.set_module_options(<module>, {<key>: <val>})` instead of `psi4.set_options({<module>__<key>: <val>})`
is deprecated, and in 1.5 it will stop working

psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py::test_json
Using `psi4.json_wrapper.run_json` instead of `psi4.schema_wrapper.run_qcschema` is deprecated, and in 1.5 it wil
l stop working

-- Docs: https://docs.pytest.org/en/stable/warnings.html
============================================= short test summary info =============================================
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py:162: Not detecting module mrcc. Install
package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py:733: Not detecting module erd. Install
package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py:783: Not detecting module cfour. Instal
l package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py:868: Not detecting module gpu_dfcc. Ins
tall package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py:1189: Not detecting module fockci. Inst
all package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py:1240: Not detecting module cct3. Instal
l package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons.py:1286: Not detecting module psixas. Inst
all package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons_qcschema.py:75: Not detecting module ipi.
Install package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_addons_qcschema.py:688: Not detecting module fock
ci. Install package if necessary to enable tests.
SKIPPED [1] psi4conda/lib/python3.8/site-packages/psi4/tests/test_mdi.py:11: Not detecting module mdi. Install pack
age if necessary to enable tests.
============== 41 passed, 10 skipped, 3313 deselected, 4 xfailed, 32 warnings in 1200.56s (0:20:00) ===============

Configuring BLAS/LAPACK
Further, as the stock BLAS/LAPACK libraries are not preferred, I have separately tried to install intel-mkl library using apt-get. How do I use CMake to link that with psi4 installed on my machine(and python modules like numpy)? or is it already done when I install psi4?

Those tests are not failing, they are skipped. Every warning message you see is about an addon that Psi4 interfaces with, but isn’t part of Psi4. It is perfectly normal to not have those add-ons.

I’m no expert on BLAS linking, so I’ll get somebody else for that question.

2 Likes

Let’s clarify if you’re after one or two installations of psi4. By downloading the installer above, bashing it, and running the tests, you’ve got a full working installation of Psi4 that’s already linked to MKL (ldd psi4conda/lib/python3.8/site-packages/psi4/core.*.so if you want to see). There’s no need for further BLAS or MKL or compiler or CMake involvement – you’re good to go.

If you additionally want to compile Psi4 from source, you can apt-get MKL and other dependencies (see here for linking BLAS Compiling and Installing from Source), but it will take hours to build the integrals. An easier way to build from source is to use the “source” directions off the installer page rather than “installer” directions. That’ll bring all your dependencies pre-compiled (can use your psi4conda conda installation or a separate one) so you’re only compiling psi4 itself. But if you just want to run Psi4, not develop it or compile a tuned copy on a computing cluster, I’d skip the build-from-source and use the installation you’ve already got running from the installer.

Thanks! I guess that answers my question.

For now, I am just trying to run it locally on my linux machine. Once, I’ve figured a few basic things, I want to use psi4 to build workflow for my MCSCF calculations, for which I plan to use the computer-cluster hosted at by my university. For that, I may have to build a optimized version on that for my work.