Installing SOLMA with OpenSuse

Question

Installing SOLMA with OpenSuse

dungqly opened this issue 7 years ago · comments

Everything is going well until...
I am trying to install SOLMA with the command line:
mvn install
(The step #4) as instructed in https://github.com/proteus-h2020/TestSolma)
I get the error as shown below. It is something about "undefined symbol: cblas_dgemm". I have already both blas and atlas installed in my computer.

If you know how to fix it please could you let me know.

I am using Suse version Leap42.1

Thanks,
Dung

[INFO] --- scalatest-maven-plugin:1.0:test (integration-test) @ proteus-solma_2.10 ---
Discovery starting.
Discovery completed in 124 milliseconds.
Run starting. Expected test count is: 4
FrequentDirectionsITSuite:
Flink's Frequent Directions
15:09:06.509 [ScalaTest-main-running-FrequentDirectionsITSuite] [ - ] WARN org.apache.flink.runtime.net.SSLUtils - Not a SSL socket, will skip setting tls version and cipher suites.
May 02, 2017 3:09:08 PM com.github.fommil.jni.JniLoader liberalLoad
INFO: successfully loaded /tmp/jniloader442498144106495151netlib-native_system-linux-x86_64.so
May 02, 2017 3:09:08 PM com.github.fommil.jni.JniLoader load
INFO: already loaded netlib-native_system-linux-x86_64.so
java: symbol lookup error: /tmp/jniloader442498144106495151netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dgemm
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 40.014 s

Ventura Del Monte · Answer 1 · Tue May 02 2017 22:47:39 GMT+0800 (China Standard Time)

Hi, it looks there is some problem with netlib (the underlying linear algebra library we use). I would suggest you to install all the dependencies listed in the Linux config section [1]

[1] https://github.com/fommil/netlib-java#linux

dungqly · Answer 2 · Wed May 03 2017 18:56:11 GMT+0800 (China Standard Time)

Hi Ventura,

sudo apt-get install libatlas3-base libopenblas-base
sudo update-alternatives --config libblas.so
sudo update-alternatives --config libblas.so.3
sudo update-alternatives --config liblapack.so
sudo update-alternatives --config liblapack.so.3

Do you know how to use those above command lines in Opensuse?

I use:
sudo zypper install libatlas3 libopenblas

But it shows something like
Loading repository data...
Reading installed packages...
'libatlas3' is already installed.
No update candidate for 'libatlas3-3.10.2-4.6.x86_64'. The highest available version is already installed.
'libopenblas' not found in package names. Trying capabilities.
No provider of 'libopenblas' found.
Resolving package dependencies...

Nothing to do

I have used YaST instead and installed all atlas and blas libs but I do not know why it shows errro
"undefined symbol: cblas_dgemm" when I use
mvn install to install SOLMA.

Nacho García Fernández · Answer 3 · Wed May 03 2017 18:59:47 GMT+0800 (China Standard Time)

Hi @dungqly

Could you try the following command?

sudo zypper install libatlas-base-dev

I think you are missing the libatlas-base-dev package, which should contain such missing symbol (cblas_dgemm)

dungqly · Answer 4 · Wed May 03 2017 19:03:41 GMT+0800 (China Standard Time)

Hi Nacho,

Here is the error when I run the command as you suggested.

dungly@suse:~> sudo zypper install libatlas-base-dev
Loading repository data...
Reading installed packages...
'libatlas-base-dev' not found in package names. Trying capabilities.
No provider of 'libatlas-base-dev' found.

dungqly · Answer 5 · Wed May 03 2017 19:08:54 GMT+0800 (China Standard Time)

In OpenSuse it seems to have a difference between "libatlas3" and "libatlas3-base"

When I use:
sudo zypper install libatlas3

Then I have this
dungly@suse:~> sudo zypper install libatlas3
Loading repository data...
Reading installed packages...
'libatlas3' is already installed.
No update candidate for 'libatlas3-3.10.2-4.6.x86_64'. The highest available version is already installed.
Resolving package dependencies...

Nothing to do

BUT if I use:
sudo zypper install libatlas3-base
then I have this

dungly@suse:~> sudo zypper install libatlas3-base
Loading repository data...
Reading installed packages...
Package 'libatlas3-base' not found.
Resolving package dependencies...

Nothing to do.

Nacho García Fernández · Answer 6 · Wed May 03 2017 19:17:57 GMT+0800 (China Standard Time)

A similar issue was reported some time ago by a OpenSuse user:
fommil/netlib-java#66

Could you try with the proposed solution? (last comment)

dungqly · Answer 7 · Wed May 03 2017 21:02:28 GMT+0800 (China Standard Time)

It seems that my new version of Atlas in Suse Leap41.1 does not have libcblas.so.3 but the older version has.

After downgrading atlas to older version I have a new error "undefined symbol: slamch_" when trying to install SOLMA:
mvn install

[INFO] --- scalatest-maven-plugin:1.0:test (integration-test) @ proteus-solma_2.10 ---
Discovery starting.
Discovery completed in 156 milliseconds.
Run starting. Expected test count is: 4
FrequentDirectionsITSuite:
Flink's Frequent Directions
13:50:01.857 [ScalaTest-main-running-FrequentDirectionsITSuite] [ - ] WARN org.apache.flink.runtime.net.SSLUtils - Not a SSL socket, will skip setting tls version and cipher suites.
May 03, 2017 1:50:03 PM com.github.fommil.jni.JniLoader liberalLoad
INFO: successfully loaded /tmp/jniloader6540861316573616181netlib-native_system-linux-x86_64.so
java: symbol lookup error: /tmp/jniloader6540861316573616181netlib-native_system-linux-x86_64.so: undefined symbol: slamch_
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE

This is what I have with ldd:

dungly@suse:> ldd /tmp/jniloader4513052076299525864netlib-native_system-linux-x86_64.so
ldd: warning: you do not have execution permission for `/tmp/jniloader4513052076299525864netlib-native_system-linux-x86_64.so'
linux-vdso.so.1 (0x00007ffc0d966000)
libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00007eff77000000)
libblas.so.3 => /usr/lib64/libblas.so.3 (0x00007eff76da7000)
liblapack.so.3 => /usr/lib64/atlas/liblapack.so.3 (0x00007eff76b83000)
libc.so.6 => /lib64/libc.so.6 (0x00007eff767db000)
libquadmath.so.0 => /usr/lib64/libquadmath.so.0 (0x00007eff7659c000)
libm.so.6 => /lib64/libm.so.6 (0x00007eff7629a000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007eff76083000)
libf77blas.so.3 => /usr/lib64/atlas/libf77blas.so.3 (0x00007eff75e62000)
libcblas.so.3 => /usr/lib64/atlas/libcblas.so.3 (0x00007eff75c3f000)
/lib64/ld-linux-x86-64.so.2 (0x000055a4a1a3d000)
libatlas.so.3 => /usr/lib64/atlas/libatlas.so.3 (0x00007eff74f5e000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007eff74d41000)
dungly@suse:> ldd /tmp/jniloader5216132806779094329netlib-native_system-linux-x86_64.so:
ldd: /tmp/jniloader5216132806779094329netlib-native_system-linux-x86_64.so:: No such file or directory

Nacho García Fernández · Answer 8 · Wed May 03 2017 21:19:41 GMT+0800 (China Standard Time)

What a mess!

What about trying to reinstall the whole netlib library?

dungqly · Answer 9 · Wed May 03 2017 21:42:23 GMT+0800 (China Standard Time)

Yes, just done it. So the error is expected as:
java: symbol lookup error: /tmp/jniloader9069070264778543719netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dgemm

Any ideas, please.

[INFO] --- scalatest-maven-plugin:1.0:test (integration-test) @ proteus-solma_2.10 ---
Discovery starting.
Discovery completed in 129 milliseconds.
Run starting. Expected test count is: 4
FrequentDirectionsITSuite:
Flink's Frequent Directions
14:38:05.950 [ScalaTest-main-running-FrequentDirectionsITSuite] [ - ] WARN org.apache.flink.runtime.net.SSLUtils - Not a SSL socket, will skip setting tls version and cipher suites.
May 03, 2017 2:38:07 PM com.github.fommil.jni.JniLoader liberalLoad
INFO: successfully loaded /tmp/jniloader9069070264778543719netlib-native_system-linux-x86_64.so
May 03, 2017 2:38:07 PM com.github.fommil.jni.JniLoader load
INFO: already loaded netlib-native_system-linux-x86_64.so
java: symbol lookup error: /tmp/jniloader9069070264778543719netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dgemm
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 36.766 s
[INFO] Finished at: 2017-05-03T14:38:07+01:00
[INFO] Final Memory: 104M/1518M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (integration-test) on project proteus-solma_2.10: There are t

Ventura Del Monte · Answer 10 · Wed May 03 2017 23:30:17 GMT+0800 (China Standard Time)

The problem is that your system does not have ATLAS and OpenBLAS libraries installed. I am not an opensuse user, therefore, I can only suggest to either build ATLAS and OpenBLAS from their source and add the libraries path to LD_LIBRARY_PATH (check their documentation), or change OS (choosing a more mainstream one, e.g., ubuntu), or use a virtual machine.

dungqly · Answer 11 · Thu May 04 2017 18:04:06 GMT+0800 (China Standard Time)

or change OS (choosing a more mainstream one, e.g., ubuntu), or use a virtual machine.

Agreed. Using Ubuntu and it works well.

Thanks a lot for your time and your suggestions @ventura and @nacho.

Regards,
Dung

l-cdc · Answer 12 · Sat Oct 07 2017 18:15:09 GMT+0800 (China Standard Time)

For future reference, I was able to solve this by installing OpenBLAS.

sudo zypper install libopenblas_openmp0
sudo update-alternatives --config libblas.so.3

Then selecting the newly installed library.

Installing SOLMA with OpenSuse

Hi Ventura,

sudo apt-get install libatlas3-base libopenblas-base sudo update-alternatives --config libblas.so sudo update-alternatives --config libblas.so.3 sudo update-alternatives --config liblapack.so sudo update-alternatives --config liblapack.so.3

After downgrading atlas to older version I have a new error "undefined symbol: slamch_" when trying to install SOLMA: mvn install

Any ideas, please.

sudo apt-get install libatlas3-base libopenblas-base
sudo update-alternatives --config libblas.so
sudo update-alternatives --config libblas.so.3
sudo update-alternatives --config liblapack.so
sudo update-alternatives --config liblapack.so.3

After downgrading atlas to older version I have a new error "undefined symbol: slamch_" when trying to install SOLMA:
mvn install