Hi,
I am trying to compile amber 24/ambertools 25 via spack (using a spack package that I wrote, which I modified from the package I wrote to successfully compile amber 22).
The cmake command it is running is (note this is created by my spack package)
'cmake' '..' '-DCMAKE_INSTALL_PREFIX=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/amber-24-ylffv4six4kfeeatemjbkkmdhlpttjvt' '-DCOMPILER=GNU' '-DMPI=FALSE' '-DCUDA=FALSE' '-DINSTALL_TESTS=TRUE' '-DDOWNLOAD_MINICONDA=TRUE' '-DPnetCDF_C_LIBRARY=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/parallel-netcdf-1.12.2-zybl47viwczmk7mgfwvl4tqb3ztjhpws/lib/libpnetcdf.so' '-DPnetCDF_C_INCLUDE_DIR=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/parallel-netcdf-1.12.2-zybl47viwczmk7mgfwvl4tqb3ztjhpws/include' '-DNetCDF_INCLUDES=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/parallel-netcdf-1.12.2-zybl47viwczmk7mgfwvl4tqb3ztjhpws/include' '-DNetCDF_LIBRARIES_F90=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/netcdf-fortran-4.5.3-n67ma7yruwcbofd3c7si3w4kdjrecogh/lib/libnetcdff.so' '-DNetCDF_INCLUDES_F90=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/netcdf-fortran-4.5.3-n67ma7yruwcbofd3c7si3w4kdjrecogh/include' '-DNetCDF_LIBRARIES_C=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/netcdf-c-4.8.1-mtfjuhhttnbkd6mycxqbjlgqptkooqh5/lib/libnetcdf.so' '-DNetCDF_INCLUDE_C=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/netcdf-c-4.8.1-mtfjuhhttnbkd6mycxqbjlgqptkooqh5/include' '-DNetCDF_LIBRARIES_C=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/netcdf-c-4.8.1-mtfjuhhttnbkd6mycxqbjlgqptkooqh5/lib/libnetcdf.so' '-DNetCDF_INCLUDE_C=/cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/netcdf-c-4.8.1-mtfjuhhttnbkd6mycxqbjlgqptkooqh5/include’
And the end of the log file is:
-- Found BISON: /cm/shared/apps/spack/0.17.3/cpu/opt/spack/linux-rocky9-cascadelake/gcc-10.2.0/bison-3.8.2-egvqhviywlssx3jqxi6ean2jvm5hgbi4/bin/bison (found version "3.8.2")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so
-- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found Perl: /usr/bin/perl (found version "5.32.1")
-- Found perl make: /usr/bin/make
-- Perl modules well be installed to AMBERHOME/lib/perl
-- Running update_amber...
PatchingError: .patches/Amber24_Unapplied_Patches/update.2 failed to apply. No changes made from this patch
CMake Error at cmake/AmberUpdater.cmake:35 (message):
update_amber failed !
See its output above.
Call Stack (most recent call first):
CMakeLists.txt:135 (include)
-- Configuring incomplete, errors occurred!
Thanks,
Jerry
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Received on Wed Oct 22 2025 - 15:30:02 PDT
