Good day,
I have installed psi4 in a cluster that uses torque to schedule jobs; initially, I installed it perfectly, but it wasn’t performing well thread-wise for ccsd calculations (something that has been discussed previously on here) so I installed quite a few mkl/lapack/blas packages via Conda and now I’m getting the following traceback
Traceback (most recent call last):
File "/home/tug63828/work/psi4/psi4conda/lib//python3.5/site-packages/psi4/__init__.py", line 55, in <module>
from . import core
ImportError: /home/tug63828/work/psi4/psi4conda/lib//python3.5/site-packages/psi4/core.so: undefined symbol: mkl_lapack_ao_dgetrf
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/path/psi4/psi4conda/bin/psi4", line 158, in <module>
import psi4
File "/path/psi4/psi4conda/lib//python3.5/site-packages/psi4/__init__.py", line 60, in <module>
raise ImportError("{0}".format(err))
ImportError: /path/psi4/psi4conda/lib//python3.5/site-packages/psi4/core.so: undefined symbol: mkl_lapack_ao_dgetrf
I’ve tried Conda update --all
and I’ve uninstalled & installed it again, but I keep getting the same problem; below is a copy of Conda list
Name Version Build Channel
_tflow_1100_select 0.0.3 mkl anaconda
absl-py 0.4.1 py35_0 anaconda
alabaster 0.7.10 py35_0
asn1crypto 0.22.0 py35_0
astor 0.7.1 py35_0 anaconda
babel 2.5.0 py35_0
blas 1.0 mkl conda-forge
bzip2 1.0.8 h7b6447c_0 anaconda
ca-certificates 2019.9.11 hecc5488_0 conda-forge
certifi 2018.8.24 py35_1001 conda-forge
cffi 1.11.5 py35he75722e_1 anaconda
chemps2 1.8.3 5
cloog 0.18.0 0
cmake 3.6.3 0
conda 4.5.11 py35_0 conda-forge
conda-env 2.6.0 1 anaconda
cryptography 1.8.1 py35_0
curl 7.54.1 0
dftd3 3.2.1 h84218bc_2
dkh 1.2 h173d85e_2
docutils 0.12 py35_2
erd 3.0.6 0
expat 2.1.0 0
gast 0.3.2 py_0 anaconda
gcc-5 5.2.0 1
gcc-5-mp 5.2.0 0
gcp 2.0.2 h84218bc_1
gdma 2.2.6 h0e1e685_6
gmp 6.1.0 0
grpcio 1.12.1 py35hdbcaa40_0 anaconda
hdf5 1.8.17 2 anaconda
icc_rt 2019.5 intel_281 intel
idna 2.6 py35_0
imagesize 0.7.1 py35_0
intel-openmp 2019.5 281 anaconda
intelpython 2019.5 0 intel
isl 0.12.2 0
jinja2 2.10.3 py_0 anaconda
krb5 1.13.2 0
lapack 3.6.1 ha44fe06_2 conda-forge
libblas 3.8.0 14_mkl conda-forge
libefp 1.5.0 h3d75fe8_3
libffi 3.2.1 h4deb6c0_3 anaconda
libgcc-ng 9.1.0 hdf63c60_0 anaconda
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0 anaconda
libint 1.2.1 hb4a4fd4_6
liblapack 3.8.0 14_mkl conda-forge
libopenblas 0.3.7 h6e990d7_3 conda-forge
libprotobuf 3.6.0 hdbcaa40_0 anaconda
libssh2 1.8.0 0
libstdcxx-ng 9.1.0 hdf63c60_0 anaconda
libxc 3.0.0 3
markdown 2.6.11 py35_0 anaconda
markupsafe 1.0 py35h14c3975_1 anaconda
mkl 2019.5 intel_281 intel
mkl-devel 2019.5 intel_281 intel
mkl-dnn 0.14 2 intel
mkl-include 2019.5 intel_281 intel
mkl-rt 11.1 p0 anaconda
mkl-service 1.1.2 py35h90e4bf4_5 anaconda
mkl-static 2019.5 intel_281 intel
mkl_fft 1.0.9 py35_0 conda-forge
mkl_random 1.0.1 py35h4414c95_1 anaconda
mpc 1.0.1 0
mpfr 3.1.2 0
ncurses 5.9 10
numpy 1.15.2 py35h1d66e8a_0 anaconda
numpy-base 1.15.2 py35h81de0dd_0 anaconda
openblas 0.3.7 h6e990d7_3 conda-forge
openmp 2018.0.3 intel_0 intel
openssl 1.0.2t h14c3975_0 conda-forge
packaging 16.8 py35_0
pcmsolver 1.1.10 py35_0
pip 10.0.1 py35_0 anaconda
protobuf 3.6.0 py35hf484d3e_0 anaconda
psi4 1.1+add49b9 py35_0
psi4-deps 1.0 py35_1
psi4-lt-mp 1.1 py35_0
py 1.4.34 py35_0
pyasn1 0.2.3 py35_0
pycosat 0.6.3 py35h14c3975_0 anaconda
pycparser 2.19 py_0 anaconda
pygments 2.4.2 py_0 anaconda
pyopenssl 17.0.0 py35_0
pyparsing 2.4.5 py_0 anaconda
pytest 3.2.1 py35_0
python 3.5.4 0 anaconda
pytz 2019.3 py_0 anaconda
readline 6.2 2
requests 2.14.2 py35_0 anaconda
ruamel_yaml 0.15.46 py35h14c3975_0 anaconda
setuptools 36.5.0 py35ha8c1747_0 anaconda
simint 0.7 h642920c_1
six 1.11.0 py35_1 anaconda
snowballstemmer 1.2.1 py35_0
sphinx 1.5.6 py35_0
sqlite 3.13.0 0 anaconda
tbb 2019.8 intel_281 intel
tcl 8.6.4 24 intel
tensorboard 1.10.0 py35hf484d3e_0 anaconda
tensorflow 1.10.0 mkl_py35heddcb22_0 anaconda
tensorflow-base 1.10.0 mkl_py35h3c3e929_0 anaconda
tensorflow-mkl 1.10.0 h067cd57_0 anaconda
termcolor 1.1.0 py35_1 anaconda
tk 8.5.18 0 anaconda
v2rdm_casscf 0.3 py35_1
werkzeug 0.16.0 py_0 anaconda
wheel 0.31.1 py35_0 anaconda
xz 5.2.4 h14c3975_4 anaconda
yaml 0.1.7 h96e3832_1 anaconda
zlib 1.2.11 h7b6447c_3 anaconda
& I have also reproduced a copy of the input file
molecule {
C 2.6372520249 0.6873075456 -0.0040048359
C 1.1501114063 0.4808993121 -0.0042726025
C 0.2449200504 1.4778951596 -0.0731787998
N -1.1222685387 1.2439401232 -0.0707227389
H -1.7819975258 2.0093256115 -0.1232858883
C -1.6880455229 -0.0153244146 0.0014545382
O -2.8905987615 -0.2139917192 0.0031835806
N -0.7399016692 -1.0246999638 0.0714707584
H -1.1086018942 -1.9694149019 0.1261276632
C 0.6551879375 -0.9034026134 0.0762078127
O 1.3671253160 -1.8940931614 0.1430932331
H 3.0842210647 0.2756879150 0.9082783889
H 3.0994944200 0.1679731539 -0.8514111939
H 2.8831484942 1.7534479350 -0.0671328362
H 0.5310514699 2.5251065170 -0.1348240943
}
memory 100 GB
set {
basis "cc-pVDZ"
reference rhf
roots_per_irrep [2]
}
energy('eom-ccsd')
properties('eom-ccsd', properties=[oscillator_strength])
any help would be tremendously appreciated.
