Hi Robert,
Have you resolved this issue? I just encountered the same issue while trying to install AMBER24 on a supercomputer’s GPU node.
My workaround is not very elegant, but it worked. Please follow exactly the steps below:
1. In build/ directory, do ./clean_build first. It may take a while.
2. Do ./run_cmake. This step will show the warning of “IMPORTED_LOCATION not set for BZip2::BZip2” as you have observed before.
3. Go to Ambertools/src and execute:
find . -type f -name "*.txt" -print0 | xargs -0 sed -i '' -e 's|BZip2::BZip2-NOTFOUND|/scratch/rdp135/bzip2/lib/libbz2.a|g' ; find . -type f -name "*.make" -print0 | xargs -0 sed -i '' -e 's|BZip2::BZip2-NOTFOUND|/scratch/rdp135/bzip2/lib/libbz2.a|g'
This step is to forcefully tell all the “BZip2::BZip2-NOTFOUND” flags to be replaced by the customized location of libbz2.a. There are only several places, so I used a script to do that text replacement automatically without disturbing other configured caches.
1. Go back to build/ (cd ../..) and then continue with make install. It should work now without being stuck at 65%.
Hope it helps.
Best regards,
Zhen.
From: David A Case via AMBER <amber.ambermd.org>
Date: Thursday, October 10, 2024 at 6:41 PM
To: Robert Palmere <rdp135.oarc.rutgers.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] BZIP2 Error when building Amber24
On Tue, Oct 08, 2024, Robert Palmere via AMBER wrote:
>
>I am encountering an issue with BZIP2 library not being completely found when installing AMBER24.
>
>cmake $AMBER_PREFIX/amber24_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
> -DCOMPILER=GNU \
> -DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=FALSE -DMVAPICH2GDR_GPU_DIRECT_COMM=TRUE \
> -DZLIB_ROOT=/home/rdp135/zlib/ -DBZIP2_LIBRARIES=/scratch/rdp135/bzip2/lib/libbz2.a -DBZIP2_INCLUDE_DIR=/scratch/rdp135/bzip2/include/ \
> -DNCCL=TRUE -DNCCL_LIBRARY=/scratch/rdp135/nccl/build/lib/libnccl_static.a -DNCCL_INCLUDE_DIR=/scratch/rdp135/nccl/build/include/ \
> 2>&1 | tee cmake.log
Is it possible for you to install libbz2 in a "standard" location, like
under /usr/lib (often in some folder like /usr/lib/x86_64-linux-gnu)?
I understand that this requires privileges, but it also avoids the problem
of having to specify the location in a way that cmake understands.
If this is not possible, trying to set an environment variable like
LD_LIBRARY_PATH might be worth exploring, as has been suggested.
...dac
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Received on Mon Nov 04 2024 - 06:30:01 PST
