BLAS/LAPACK Linking Issues

[iris-garden]

Note

The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.

(Aug 07, 2023 at 02:08) sk4 said:

Hi!

I have been running into issues with BLAS/LAPACK linking when runing Hail functions that use linear algebra operations like linear regression or PCA. The error message looks like this:

symbol lookup error: /tmp/jniloader421303948191888475netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dgemv

I have tried the fixes proposed in this forum:

While running a GWAS / linear regression I get: "Answer from Java side empty" and "undefined symbol: cblas_dgemv"

I’m getting this error when I try to run a simple GWAS
/apps/well/java/jdk1.8.0_latest/bin/java: symbol lookup error: /tmp/jniloader1259648657693918558netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dgemv
ERROR:root:Exception while sending command.
Traceback (most recent call last):
File "/well/lindgren/UKBIOBANK/nbaya/conda/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1159, in send_command
raise Py4JNetworkError("Answer from Java side is empty")
py4j.pr…

and this one:

Undefined symbol: cblas_dgemm

Hi!
I get the following error when I execute pipelines including linear_regression_rows:
/usr/java/default/bin/java: symbol lookup error: /.../...netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dgemv

How do I avoid this error?

But neither have worked to resolve the issue. In particular, if I try the “quick fix” to set LD_PRELOAD to the OpenBLAS path, I get an error from NumPy when importing Hail before initialization:

RuntimeError: The current Numpy installation ('/nfs/sw/hail/hail-0.2/python/lib/python3.9/site-packages/numpy/__init__.py') fails to pass simple sanity checks. This can be caused for example by incorrect BLAS library being linked in, or by mixing package managers (pip, conda, apt, ...). Search closed numpy issues for similar problems.

Is there another way to resolve this issue?

[iris-garden]

Note

The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.

(Aug 07, 2023 at 14:26) danking said:

sk4 ,

What environment are you in? Do you have root privileges on these machines?

Are you certain you have OpenBLAS installed? You need a copy of open blas with the name libblas.so and you need to convince netlib to load that not something else. Did you already try both of these approaches?

mkdir -p ~/lib
ln -s /path/to/your/libopenblas.so ~/lib/libblas.so
export LD_LIBRARY_PATH=~/lib:$LD_LIBRARY_PATH

and starting Spark with this?

--conf spark.executor.extraClassPath="/path/to/libblas.so:/path/to/liblapack.so"

The hl.init approach only works if the Spark cluster isn’t already running.

[iris-garden]

Note

The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.

(Aug 07, 2023 at 16:53) sk4 said:

Hi danking,

Well, it looks like the Spark --conf flag approach works now when using spark-submit. I tried it earlier along with the symlink approach, but perhaps I didn’t specify the OpenBLAS and LAPACK paths correctly. Thanks for your quick response!

[iris-garden]

Note

The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.

(Nov 09, 2023 at 03:51) sk4 said:

Hi danking,

It appears that the BLAS linking issue isn’t fully solved for me. While setting the --conf flag to point to the OpenBLAS/LAPACK paths when running spark-submit works for hl.hwe_normalized_pca, the same setting doesn’t work for hl.logistic_regression_rows. I’ve tried different settings based on the fixes you suggested, but none of them have worked so far.

Option 1: set the --conf path to directly point to OpenBLAS/LAPACK, i.e.

--conf spark.executor.extraClassPath=/usr/lib64/libopenblas.so:/usr/lib64/liblapack.so

Option 2: create symlinks to OpenBLAS/LAPACK and add to LD_LIBRARY_PATH, i.e.

ln -s /usr/lib64/libopenblas.so ~/lib/libblas.so`
ln -s /usr/lib64/liblapack.so ~/lib/liblapack.so`
export LD_LIBRARY_PATH=~/lib:$LD_LIBRARY_PATH

Option 3: set the --conf path to point to the symlink for OpenBLAS/LAPACK, i.e.

--conf spark.executor.extraClassPath=~/lib/libblas.so:~/lib/liblapack.so

Option 4: enable both Option 2 + 3

This is the example I’m trying to run, initially posted in this forum:

While running a GWAS / linear regression I get: "Answer from Java side empty" and "undefined symbol: cblas_dgemv"

I’m getting this error when I try to run a simple GWAS /apps/well/java/jdk1.8.0_latest/bin/java: symbol lookup error: /tmp/jniloader1259648657693918558netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dgemv ERROR:root:Exception while sending command. Traceback (most recent call last): File "/well/lindgren/UKBIOBANK/nbaya/conda/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1159, in send_command raise Py4JNetworkError("Answer from Java side is empty") py4j.pr…

import hail as hl
hl.init(log='hail.log')
mt = hl.balding_nichols_model(1,100,2)
mt = mt.annotate_cols(y = hl.rand_bool(0.5))
result_ht = hl.logistic_regression_rows(
	test='wald',
	y=mt.y, 
	x=mt.GT.n_alt_alleles(), 
	covariates=[1]
)

I don’t have root privileges on the server I’m using, and Hail is loaded through a modulefile (though I load Spark/Java dependencies separately). In general, I start the Spark server first before initializing Hail with spark-submit, so hl.init(spark_conf=...) wouldn’t work like you mentioned. Is there any other fix that could work for this issue?