Spades fails to compile from source on an aws r7i.2xlarge instance

[wiebepo]

Description of bug

We migrated our Jenkins server to an r7i.2xlarge instance (8 vCPU, 64 GiB, DDR5 memory). One of our Jenkins jobs includes building spades from source. Here is an excerpts of the docker file:

FROM library/ubuntu:22.04

RUN apt-get update && \
    apt-get upgrade -y && \
    apt-get install -y libbz2-dev liblz1 g++ cmake python-is-python3

RUN git clone --quiet https://github.com/ablab/spades.git -b main &&   \
    cd spades && \
    PREFIX=/usr/local ./spades_compile.sh && \
    cd .. &&   \
    rm -fr spades && \
    spades.py --test

spades.log

spades.log

params.txt

no log available. Failure occurs during compilation.

SPAdes version

SPades version 4.0.0

Operating System

Ubuntu 22.04

Python Version

3.10.12

Method of SPAdes installation

compile from source

No errors reported in spades.log

• [X] Yes

[asl]

@wiebepo Does this reproduce only on this kind of instance? And no problem on smaller ones?

[wiebepo]

@wiebepo Does this reproduce only on this kind of instance? And no problem on smaller ones?

We cloned the server on an r6i.2xlarge instance, and the job succeeds. It is the predecessor and is also 8 vCPUs and 64 GiB RAM; however, it uses DDR4 memory. Not sure if this matters.

[wiebepo]

FWIW this error from the attached log seemed to be the most relevant:

/spades/ext/include/blaze/blaze/system/CacheSize.h:77:1: error: static assertion failed: Compile time condition violated 77 | BLAZE_STATIC_ASSERT( blaze::cacheSize > 100000UL && blaze::cacheSize < 100000000UL ); | ^~~~~~~~~~~~~~~~~~~

[asl]

FWIW this error from the attached log seemed to be the most relevant:

Yes, exactly. This is why I asked if the problem reproduced on smaller instance.

[asl]

Will you please provide the output of the following commands on that instance?

cat /sys/devices/system/cpu/cpu0/cache/index3/size
cat /sys/devices/system/cpu/cpu0/cache/index2/size
cat /sys/devices/system/cpu/cpu0/cache/index1/size

Thanks!

[wiebepo]

Added to the dockerfile, and rerun:

RUN cat /sys/devices/system/cpu/cpu0/cache/index3/size && \
    cat /sys/devices/system/cpu/cpu0/cache/index2/size && \
    cat /sys/devices/system/cpu/cpu0/cache/index1/size

Output:

107520K 2048K 32K

[asl]

I filled upstream issue with blaze, let's see what they will say. IMO this static assert does not make much sense

[asl]

@wiebepo This should be fixed in main just in case. Upstream sadly seems to be dead...