GWAS tutorial problem with java

This issue was initially reported at the github site: GWAS tutorial problem with java · Issue #9939 · hail-is/hail · GitHub. I was told to come here for the discussion. Please click the link for details. To brief, we are trying to run the GWAS tutorial and see some problems with java gateway, which is weird. The reply from Danking is that maybe we had not installed all the necessary packages?

Here are some updates:

  • At the time we reported the issue, openBlas was not installed, so we later on installed it
  • Now we have java-jdk8.0.92, python 3.7.9, openblas 0.3.10, blas 1.0, lapack 3.6.0, gcc 7.3.0.

Now we are still having the following error:

/usr/lib/jvm/java-1.8.0-openjdk- symbol lookup error: /tmp/ undefined symbol: cblas_dgemm

ERROR:root:Exception while sending command.

My system admin said maybe the issue is that our os (redhat) does not have the latest packages required to run hail? Our os version, as given by “uname -a” is the following:

Linux lnx009 3.10.0-1160.6.1.el7.x86_64 #1 SMP


@johnc1231 I think you have the most context for this?

We have a guide to this problem: