[Install]: CPU Spack installation

[EmilyBourne]

Issue Description

Linker issue. E.g:

/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `stbmv_thread_NUU'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `ztrmv_thread_RUN'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `ctrmv_thread_RUN'
/usr/bin/ld: /lib/x86_64-linux-gnu/liblapack.so.3: undefined reference to `strtrs_UNN_parallel'
/usr/bin/ld: /lib/x86_64-linux-gnu/liblapack.so.3: undefined reference to `ztrtri_LU_parallel'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `ctbmv_thread_TLN'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `zgemv_thread_u'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `zger_thread_V'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `stpmv_thread_TUN'
/usr/bin/ld: /lib/x86_64-linux-gnu/liblapack.so.3: undefined reference to `dtrtri_UN_parallel'
/usr/bin/ld: /lib/x86_64-linux-gnu/liblapack.so.3: undefined reference to `ctrtrs_UCN_parallel'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `zgemm_thread_rt'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `cgemv_thread_r'
/usr/bin/ld: /lib/x86_64-linux-gnu/liblapack.so.3: undefined reference to `dtrtrs_LNN_parallel'
/usr/bin/ld: /lib/x86_64-linux-gnu/liblapack.so.3: undefined reference to `ctrtrs_UTU_parallel'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `dsyr_thread_L'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `cspr2_thread_L'
/usr/bin/ld: /lib/x86_64-linux-gnu/liblapack.so.3: undefined reference to `ctrtrs_LNN_parallel'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `gemm_thread_m'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `stpmv_thread_NUN'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `cgemm3m_thread_cc'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `ssymm_thread_LU'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `sgemm_thread_nt'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `ctrmv_thread_CLN'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `zhemm_thread_LL'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `cgbmv_thread_n'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `chemv_thread_M'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `cgemm3m_thread_tt'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `ctpmv_thread_CUU'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `ztpmv_thread_NLN'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `zhpr_thread_U'
/usr/bin/ld: /lib/x86_64-linux-gnu/liblapack.so.3: undefined reference to `dgetrs_N_parallel'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `zhemv_thread_V'
/usr/bin/ld: /lib/x86_64-linux-gnu/libblas.so.3: undefined reference to `chemm_thread_RU'

It seems the wrong lapack/blas is found

Steps Taken

No response

Version of the code used

ebourne_342_polar_bsplines_on_gpu branch (up to date with devel)

Environment

Ubuntu 24.04 (recent update), personal computer CPU installation

[EmilyBourne]

It seems that openblas is installed but this does not provide a liblapack.so so the version already on my computer is being used instead

[EmilyBourne]

This can be fixed locally by changing:

gyselalibxx/CMakeLists.txt

Line 56 in 71909a9

find_package(LAPACK REQUIRED)

to:

find_package(LAPACK REQUIRED BLA_VENDOR OpenBLAS)

[tpadioleau]

I think a question is why it ends up using the system blas instead of the Spack provided blas ?

[tpadioleau]

Should be reproducible with a container Ubuntu 24.04 with lapack installed from the system ?

[tpadioleau]

Can you specify the first target that encounters this problem ? So that we can do cmake --build build --target some_target

[EmilyBourne]

The first target seems to be: spline_interpolator_rtheta_tests
But you can already see the issue when you run cmake:

-- A cache variable, namely LAPACKE_DIR, has been set to specify the install directory of LAPACKE
-- Looking for LAPACKE_dgeqrf
-- Looking for LAPACKE_dgeqrf - not found
-- Looking for lapacke : test with lapack fails
-- Looking for LAPACKE_dgeqrf
-- Looking for LAPACKE_dgeqrf - found
-- Found LAPACKE: /usr/lib/x86_64-linux-gnu/liblapacke.so  

which should be:

-- A cache variable, namely LAPACKE_DIR, has been set to specify the install directory of LAPACKE
-- Looking for LAPACKE_dgeqrf
-- Looking for LAPACKE_dgeqrf - found
-- Looking for lapacke: test with lapack succeeds
-- Found LAPACKE: /home/emily/Code/spack-0.23.1/var/spack/environments/gyselalibxx-env/.spack-env/view/lib/libopenblas.so;-lm;-ldl  

In the version that works I also see:

-- Found BLAS: /home/emily/Code/spack-0.23.1/var/spack/environments/gyselalibxx-env/.spack-env/view/lib/libopenblas.so
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /home/emily/Code/spack-0.23.1/var/spack/environments/gyselalibxx-env/.spack-env/view/lib/libopenblas.so;-lm;-ldl

which I don't have at all in the broken configuration

[tpadioleau]

So the issue comes from the update to 24.04 ? Can you give more details on the differences between the two environments ?

[EmilyBourne]

So the issue comes from the update to 24.04 ? Can you give more details on the differences between the two environments ?

I don't think so. I wasn't using spack before the update. I was having problems with my installations (because I messed up my various Pythons during the upgrade) so I decided to use spack as it is isolated from the rest. I have since cleaned up my Python mess and everything seems to be back to normal but I can't exclude that I messed something else up during the upgrade

[tpadioleau]

Naive comment but, do you need the system blas/lapack ? :)

[EmilyBourne]

Naive comment but, do you need the system blas/lapack ? :)

Given that Gysela is the only library that I compile with spack I would say yes for at least 2 projects

[EmilyBourne]

But I didn't install after the upgrade so I don't know if these are working versions, leftovers from 22.04 or just something broken. I haven't tried to use them elsewhere yet