Nightly update from fresh install leads to undefined symbol: __svml_sin4

I am attempting to run some SAPT0 calculations involving iodine with ECP with Psi4 1.1. The version fresh out of psi4conda will not complete the calculation with a custom basis set with ECP:

==> Induction <==

Ind20,u (A<-B)      =    -0.009175512550 [Eh]
Ind20,u (B<-A)      =    -0.004691394009 [Eh]
Ind20,u             =    -0.013866906559 [Eh]
Exch-Ind20,u (A<-B) =     0.008725314577 [Eh]
Exch-Ind20,u (B<-A) =     0.004408616748 [Eh]
Exch-Ind20,u        =     0.013133931325 [Eh]

==> CPHF Iterations <==

Maxiter     =          50
Convergence =   1.000E-08

-----------------------------------------
Iter   Monomer A    Monomer B    Time [s]
-----------------------------------------
1      1.194E-01    2.745E-02           0
2      2.107E-02    6.354E-03           0
3      1.543E-02    2.824E-03           1
4      5.077E-03    1.009E-03           1
5      2.317E-03    2.908E-04           1
6      1.209E-03    1.058E-04           1
7      6.499E-04    2.009E-05           1
8      1.150E-03    3.653E-06           1
9      1.100E-03    1.905E-06           1
10     2.252E-03    4.741E-07           1
11     8.014E-03    9.685E-08           1

Traceback (most recent call last):
File “/home/svu/user4/psi4conda/bin/psi4”, line 248, in
exec(content)
File “”, line 62, in
File “/home/svu/user4/psi4conda/lib//python3.6/site-packages/psi4/driver/driver.py”, line 460, in energy
wfn = procedures[‘energy’][lowername](lowername, molecule=molecule, **kwargs)
File “/home/svu/user4/psi4conda/lib//python3.6/site-packages/psi4/driver/procrouting/proc.py”, line 3516, in run_fisapt
fisapt_wfn = core.fisapt(ref_wfn)

RuntimeError:
Fatal Error: Monomer A: A Matrix is not SPD
Error occurred in file: /scratch/psilocaluser/conda-builds/psi4_1495014881710/work/psi4/src/psi4/fisapt/fisapt.cc on line: 4790
The most recent 5 function calls were:

psi::PsiException::PsiException(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char const*, int)
psi::fisapt::CPHF_FISAPT::compute_cphf()
psi::fisapt::FISAPT::ind()
psi::fisapt::FISAPT::compute_energy()
psi::fisapt::fisapt(std::shared_ptrpsi::Wavefunction, psi::Options&)

*** Psi4 encountered an error. Buy a developer more coffee!
*** Resources and help at GitHub - psi4/psi4: Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python.
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The calculation will run fine if an all-electron basis set containing iodine (ADZP) is used, though I specifically would like to work with ECPs.

Updating to the nightly build from a fresh install using

conda update psi4 -c psi4/label/dev

prompts:

The following NEW packages will be INSTALLED:

gau2grid:   0.1-0
pip:        9.0.1-py36_1
wheel:      0.29.0-py36_0

The following packages will be UPDATED:

conda:      4.3.18-py36_0                     --> 4.3.30-py36h5d9f9f4_0
mkl:        2017.0.1-0                        --> 2017.0.3-0
psi4:       1.1+add49b9-py36_0 psi4/label/dev --> 1.2a1.dev781+837e345-py36_0
psi4-lt-mp: 1.1-py36_0                        --> 1.2a1.dev5-py36_0

and using

conda update psi4 libefp libint erd simint pcmsolver chemps2 gdma dkh libxc -c psi4/label/dev

prompts the following:

The following NEW packages will be INSTALLED:

gau2grid:   0.1-0
pip:        9.0.1-py36_1
wheel:      0.29.0-py36_0

The following packages will be UPDATED:

chemps2:    1.8.3-5                           --> 1.8.4-0
conda:      4.3.18-py36_0                     --> 4.3.30-py36h5d9f9f4_0
dkh:        1.2-0                             --> 1.2-h173d85e_2
erd:        3.0.6-0                           --> 3.0.6-1
gdma:       2.2.6-2                           --> 2.2.6-hf4d0741_5
libefp:     1.4.2-0                           --> 1.5b1-0
libint:     1.2.1-0                           --> 1.2.1-h73b9bb0_3
libxc:      3.0.0-3                           --> 3.0.0-6
mkl:        2017.0.1-0                        --> 2017.0.3-0
pcmsolver:  1.1.10-py36_0                     --> 1.1.10-py36_1
psi4:       1.1+add49b9-py36_0 psi4/label/dev --> 1.2a1.dev781+837e345-py36_0
psi4-lt-mp: 1.1-py36_0                        --> 1.2a1.dev5-py36_0
simint:     0.7-0                             --> 0.7-h642920c_1

When either update is completed, the following error is generated when psi4 is run:

Traceback (most recent call last):
File “/home/svu/user4/psi4conda/lib//python3.6/site-packages/psi4/init.py”, line 54, in
from . import core
ImportError: /home/svu/user4/psi4conda/lib//python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/svu/user4/psi4conda/bin/psi4”, line 158, in
import psi4
File “/home/svu/user4/psi4conda/lib//python3.6/site-packages/psi4/init.py”, line 59, in
raise ImportError(“{0}”.format(err))
ImportError: /home/svu/user4/psi4conda/lib//python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

This is my conda list:

packages in environment at /home/svu/user4/psi4conda:

asn1crypto 0.22.0 py36_0
cffi 1.10.0 py36_0
chemps2 1.8.4 0 psi4/label/dev
cloog 0.18.0 0
conda 4.3.30 py36h5d9f9f4_0
conda-env 2.6.0 0
cryptography 1.8.1 py36_0
dftd3 3.2.0 7
dkh 1.2 h173d85e_2 psi4/label/dev
erd 3.0.6 1 psi4/label/dev
gau2grid 0.1 0 psi4/label/dev
gcc-5 5.2.0 1
gcc-5-mp 5.2.0 0
gcp 2.0.1 0
gdma 2.2.6 hf4d0741_5 psi4/label/dev
gmp 6.1.0 0
hdf5 1.8.17 1
idna 2.5 py36_0
isl 0.12.2 0
libefp 1.5b1 0 psi4/label/dev
libffi 3.2.1 1
libint 1.2.1 h73b9bb0_3 psi4/label/dev
libxc 3.0.0 6 psi4/label/dev
mkl 2017.0.3 0
mpc 1.0.1 0
mpfr 3.1.2 0
numpy 1.12.1 py36_0
openssl 1.0.2k 2
packaging 16.8 py36_0
pcmsolver 1.1.10 py36_1 psi4/label/dev
pip 9.0.1 py36_1
psi4 1.2a1.dev781+837e345 py36_0 psi4/label/dev
psi4-lt-mp 1.2a1.dev5 py36_0 psi4/label/dev
psi4-rt 1.1 py36_0
py 1.4.33 py36_0
pycosat 0.6.2 py36_0
pycparser 2.17 py36_0
pyopenssl 17.0.0 py36_0
pyparsing 2.1.4 py36_0
pytest 3.0.7 py36_0
python 3.6.1 2
readline 6.2 2
requests 2.14.2 py36_0
ruamel_yaml 0.11.14 py36_1
setuptools 27.2.0 py36_0
simint 0.7 h642920c_1 psi4/label/dev
six 1.10.0 py36_0
sqlite 3.13.0 0
tk 8.5.18 0
v2rdm_casscf 0.3 py36_1
wheel 0.29.0 py36_0
xz 5.2.2 1
yaml 0.1.6 0
zlib 1.2.8 3

Would greatly appreciate any help regarding this matter. Thanks!

This issue is likely related and should help you.

Thanks for the reference! A clean environment install worked, though for anyone else who’s visiting this thread for the same reason that a miniconda dev install works but a normal anaconda dev install does not work (even when creating a new environment in anaconda). I’m not sure what packages in the anaconda install conflict with psi4, but perhaps its the gcc-5 and gcc-5-mp that loriab suggested in the other thread, since it is missing from the miniconda build.

Glad it’s working now. I made a few notes here.