I’ve been struggling to instal deal.ii on a new HPC through Candi and I’ve consistently been getting this error:
"Include /home/college/ag423y/bin/tmp/unpack/deal.II-v9.4.2/cmake/setup_finalize.cmake
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
– Unable to compile a simple test program. Trying to drop “-fuse-ld=gold” from the linker flags.
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
CMake Error at cmake/setup_finalize.cmake:137 (MESSAGE):
Configuration error: Cannot compile a test program with the final set of
compiler and linker flags:
CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wmissing-braces -Woverloaded-virtual -Wpointer-arith -Wsign-compare -Wsuggest-override -Wswitch -Wsynth -Wwrite-strings -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix -Wno-psabi -Wno-class-memaccess -fopenmp-simd -Wno-parentheses -Wno-unused-local-typedefs -O0 -ggdb -Wa,--compress-debug-sections
LD flags (DEBUG): -rdynamic -ggdb"
My PETSc version is 3.16.4 and my version of GNU make is older than 4.0.0 which I realise are quite old!
Could this be gnu id issue because my version is so old? And if so is there a work around it? because my IT admin are bit hesitant when it comes to updates.
I’ve also double checked that my modules are loaded (openmpi/1.10.7 & gcc/9.3.0) and that I’ve set the right compiler variables. I’m also excluding all the packages in Candi except for Trilinos, p4est, deal.ii and hdf5. And I’ve deleted all pervious folders with previous attempts at installation so my directory is completely clean.
Any suggestions or comments on how to resolve this would be really appreciated
The local cluster I use has Centos7, and I don’t recall seeing this error with deal.II 9.4.0 installed via candi.
One question - you mention PETSc 3.16.4. In what capacity is that being used if it is not installed with deal.II?
I’m not sure the make version (did you mean cmake?) is an issue - if the version of cmake is too old, deal.II builds a new version (at least that is what I recall).
If you can’t find a solution soon either myself or someone else using the cluster can try building with deal.II 9.4.2 and see if we can reproduce the error.
When building deal.ii this is what I get printed to screen:
“This is CMake 3.20.5”
Similarly PETSc is also being installed with deal.ii but during the configuration stages I get the two following warnings:
“++++++++++++++++++++++++++++++++++++++++++++++++++++++
The version of PETSc you are using is out-of-date, we recommend updating to a new the release Available Version: 3.18.4 Installed Version: 3.16.4 https://petsc.org/release/download/
++++++++++++++++++++++++++++++++++++++++++++++++++++++”
and
“*****WARNING: You have a version of GNU male older than 4.0. It will work but may not support all parallel testing options. You can install the --download-make-option to get the latest GNU make *****”
I should mention that I am installing candi using the following command:
The instructions in the ASPECT manual fail to mention that you don’t need most of the dependencies it tries to install, which include PETSc. If you go into the candi.cfg, you can disable everything except “p4est”, “trilinos”, “hdf5”, and “deal.II”.
Besides, the “out of date warning” is something you can safely ignore.
./candi_configure: line 122: cmake: command not found”
I would guess that the cluster has “cmake” but you might need to load a module to get it. Otherwise, you can also install a version through candi (also see candi.cfg and uncomment that line), but I would go with the system install first.
Thanks Timo, this resolved the cmake and the PETSc issues but I’m still getting the original error:
"-- Include /home/college/ag423y/dealii-candi/tmp/unpack/deal.II-v9.4.2/cmake/configure/configure_50_vectorization.cmake
– Include /home/college/ag423y/dealii-candi/tmp/unpack/deal.II-v9.4.2/cmake/setup_cpack.cmake
– Include /home/college/ag423y/dealii-candi/tmp/unpack/deal.II-v9.4.2/cmake/setup_custom_targets.cmake
– Include /home/college/ag423y/dealii-candi/tmp/unpack/deal.II-v9.4.2/cmake/setup_finalize.cmake
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
– Unable to compile a simple test program. Trying to drop “-fuse-ld=gold” from the linker flags.
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
CMake Error at cmake/setup_finalize.cmake:137 (MESSAGE):
Configuration error: Cannot compile a test program with the final set of
compiler and linker flags:
CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wmissing-braces -Woverloaded-virtual -Wpointer-arith -Wsign-compare -Wsuggest-override -Wswitch -Wsynth -Wwrite-strings -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix -Wno-psabi -Wno-class-memaccess -fopenmp-simd -Wno-parentheses -Wno-unused-local-typedefs -O0 -ggdb -Wa,--compress-debug-sections
LD flags (DEBUG): -rdynamic -ggdb"
Small update: I have managed to install deal.ii, trilinos & p4est separately by running:
./candi.sh --packages=“p4est” -j13
and so on for each of the packages.
This worked fine without throwing any errors. I’m not sure why installing the packages individually works but trying to install them together through (commenting out all the other packages) ./candi.sh --platform=deal.II-toolchain/platforms/supported/centos7.platform -j12 throws the error above!
This resolves the cmake issue and everything goes on as normal until we get to the usual stage:
Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
and then it throws the same error as above. Reposted here for continuity:
"Include /home/college/ag423y/dealii-candi/tmp/unpack/deal.II-v9.4.2/cmake/setup_finalize.cmake
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
– Unable to compile a simple test program. Trying to drop “-fuse-ld=gold” from the linker flags.
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
– Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
CMake Error at cmake/setup_finalize.cmake:137 (MESSAGE):
Configuration error: Cannot compile a test program with the final set of
compiler and linker flags:
CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wmissing-braces -Woverloaded-virtual -Wpointer-arith -Wsign-compare -Wsuggest-override -Wswitch -Wsynth -Wwrite-strings -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix -Wno-psabi -Wno-class-memaccess -fopenmp-simd -Wno-parentheses -Wno-unused-local-typedefs -O0 -ggdb -Wa,--compress-debug-sections
LD flags (DEBUG): -rdynamic -ggdb"
I’ve attached the CMakeError.log but
/home/college/ag423y/dealii-candi/tmp/build/deal.II-v9.4.2/detailed.log does not exist (you can the contents of my /home/college/ag423y/dealii-candi/tmp/build in the image attached)
