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Reach Biomedical Information Extraction
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/lib64/libc.so.6: version `GLIBC_2.14' not found #713

Closed sateeshperi closed 3 years ago

sateeshperi commented 3 years ago

I am trying to run the FAT jar of reach on HPC and get the following error. It works fine on VM where I assemble the fat jar. 

Suppressed: java.lang.NoClassDefFoundError: Could not initialize class edu.cmu.dynet.internal.dynet_swigJNI
        ... 35 more
        Suppressed: java.lang.UnsatisfiedLinkError: /tmp/dynet816865678061882470.dll: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/dynet816865678061882470.dll)
kwalcock commented 3 years ago

Here is an old email I have about that error. I haven't closely followed the updates on UA's HPCs to know whether simply moving to the other one would solve it or not (if there still are two). A docker container could provide the necessary version if necessary.

The HPCs have El Gato and Ocelote with different versions of their
operating systems.  Ocelote's is older, despite seeming to be a newer
machine, and its version of CLIBC was too old for fatdynet.  Fan moved
to El Gato and the program ran without change.  She wasn't in a
container, though.  If a container is involved, it may be supplying
GLIBC.  I went back as far as Ubuntu 14 when building fatdynet, but if
it continues to be a problem, I could try for earlier.
sateeshperi commented 3 years ago

The El Gato and Puma compute nodes have no java/8/ module available for executing the fat jar.

I tried installing glibc as per the instructions here but, was unsuccessful

please see my notebook with error logs Here

kwalcock commented 3 years ago

The unavailability of Java on El Gato may not be accurate. It seems to be preinstalled and I'm fairly sure this was the machine we've run on before.

[kalcock@gpu64 Projects]$ java -version
openjdk version "1.8.0_262"
OpenJDK Runtime Environment (build 1.8.0_262-b10)
OpenJDK 64-Bit Server VM (build 25.262-b10, mixed mode)
[kalcock@gpu64 Projects]$ ldd libdynet_swig.so 
    linux-vdso.so.1 =>  (0x00007ffc22d84000)
    libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fed43184000)
    libm.so.6 => /lib64/libm.so.6 (0x00007fed42e82000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fed42c6c000)
    libc.so.6 => /lib64/libc.so.6 (0x00007fed4289e000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fed43da2000)
MihaiSurdeanu commented 3 years ago

Thanks Keith!

kwalcock commented 3 years ago

https://public.confluence.arizona.edu/display/UAHPC/Software+Resources says that Puma has Java pre-installed, but it doesn't say which version. Have you checked it out?

sateeshperi commented 3 years ago

Thank you @kwalcock I can confirm that java/8 is pre-installed on elgato and puma and it works now.