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Archlinux: Slycot compiled against MKL crashes #138
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Hi, I doubt that it is the specific test. Try running with
pytest -k "not test_ab01"and it will fail with the next one.The error message looks like your MKL installation is incomplete.
Reacted by Akash Patel- changed the title
[-]test_ab01.py fails[/-][+]test_ab01.py fails when intel-mkl is installed[/+]on Oct 2, 2020 If you search for
undefined symbol: mkl_sparse_optimize_bsr_trsm_i8you find a lot of similar issues and forum threads. Make sure to align your numpy, intel-mkl and python-slycot packages. AUR has python-numpy-mkl. Maybe that helps.I also just tried to build slycot on Archlinux with intel-mkl installed:
- By default, the build still finds and builds against openblas, not MKL.
- With
MKLROOT=/opt/intel/mkl BLA_VENDOR=Intel10_64lp makepkg -CfI can reproduce the crash during the check() phase.
By default, the build still finds and builds against openblas, not MKL.
hmm weird that doesn't seem to be happening for me.
I think for now I'll stick with the pip package instead of using the AUR package.
I think for now I'll stick with the pip package instead of using the AUR package.
And that one finds and builds against MKL fine? Can you post the buildlog?
Note that the AUR package is the PyPI source package plus a recipe how to build it for the Archlinux system. We do not provide wheels.
If you need it precompiled, use conda. Alternatovely you can try https://build.opensuse.org/package/show/home:bnavigator:archlinux/python-slycot. In that repo, I am also preparing a
python-slycot-mklpackage usingpython-{scipy,numpy}-mkl-bin. Maybe that works for you. Unfortunately I cannot build the AUR packagepython-scipy-mklfrom source in that repo, because that would require redistributing the commercial intel tools to the public build service and violate license terms.And that one finds and builds against MKL fine? Can you post the buildlog?
For the pip package I am not building it just using
pip install slycotto get the precompiled binary. Edit: ah maybe I am misunderstanding the pypi package then.Collecting slycot Using cached slycot-0.4.0.0.tar.gz (1.5 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing wheel metadata: started Preparing wheel metadata: finished with status 'done' Collecting numpy Using cached numpy-1.19.2-cp38-cp38-manylinux2010_x86_64.whl (14.5 MB) Building wheels for collected packages: slycot Building wheel for slycot (PEP 517): started Building wheel for slycot (PEP 517): finished with status 'done' Created wheel for slycot: filename=slycot-0.4.0-cp38-cp38-linux_x86_64.whl size=1426908 sha256=2780a985c71eaf4d042bbcb724fbf443d7ad12d835f158affb918bfcb658d6ef Stored in directory: /home/acxz/.cache/pip/wheels/bf/b4/5b/1912a29df9f054ab7df4ead6506a081ca21ea9ea0ea66f3292 Successfully built slycot Installing collected packages: numpy, slycot Successfully installed numpy-1.19.2 slycot-0.4.0In any case I am more interested in getting the AUR package working with the build log here:
AUR build log
:: �[1mThere are 2 providers available for python-slycot: :: �[1mRepository AUR �[0m1) python-slycot 2) python-slycot-git �[0m Enter a number (default=1): :: �[1mChecking for conflicts...�[0m :: �[1mChecking for inner conflicts...�[0m [Aur:1] python-slycot-0.4.0.0-1 :: �[1mDownloaded PKGBUILD (1/1): python-slycot�[0m 1 python-slycot (Build Files Exist) ==> Diffs to show? ==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4) ==> :: �[1m(1/1) Parsing SRCINFO: python-slycot�[0m ==> Making package: python-slycot 0.4.0.0-1 (Fri 02 Oct 2020 12:33:37 PM EDT) ==> Retrieving sources... -> Downloading slycot-0.4.0.0.tar.gz... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1510k 100 1510k 0 0 6241k 0 --:--:-- --:--:-- --:--:-- 6241k ==> Validating source files with sha256sums... slycot-0.4.0.0.tar.gz ... Passed ==> Making package: python-slycot 0.4.0.0-1 (Fri 02 Oct 2020 12:33:39 PM EDT) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> Retrieving sources... -> Found slycot-0.4.0.0.tar.gz ==> Validating source files with sha256sums... slycot-0.4.0.0.tar.gz ... Passed ==> Removing existing $srcdir/ directory... ==> Extracting sources... -> Extracting slycot-0.4.0.0.tar.gz with bsdtar ==> Sources are ready. ==> Making package: python-slycot 0.4.0.0-1 (Fri 02 Oct 2020 12:33:41 PM EDT) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> WARNING: Using existing $srcdir/ tree ==> Starting build()... Not searching for unused variables given on the command line. -- The C compiler identification is GNU 10.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- The Fortran compiler identification is GNU 10.2.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 - yes -- Configuring done -- Generating done -- Build files have been written to: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_cmake_test_compile/build -- The C compiler identification is GNU 10.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- The Fortran compiler identification is GNU 10.2.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 - yes -- Found PythonLibs: /usr/lib/libpython3.8.so (found version "3.8.5") -- Found PythonInterp: /usr/bin/python (found version "3.8.5") -- Found NumPy: /usr/lib/python3.8/site-packages/numpy/core/include (found version "1.19.2") -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /opt/intel/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/mkl/lib/intel64_lin/libmkl_core.so;/usr/lib/libgomp.so;-lpthread;-lm;-ldl -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. -- NumPy: /usr/lib/python3.8/site-packages/numpy/core/include -- LAPACK: /opt/intel/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/mkl/lib/intel64_lin/libmkl_core.so;/usr/lib/libgomp.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl -- BLAS: /opt/intel/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/mkl/lib/intel64_lin/libmkl_core.so;/usr/lib/libgomp.so;-lpthread;-lm;-ldl -- Slycot version: 0.4.0 -- Found F2PY: /usr/bin/f2py3 (found version "2") -- Performing Test Weak Link MODULE -> SHARED (gnu_ld_ignore) - Success _modinit_prefix:PyInit_ -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: SKBUILD -- Build files have been written to: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build Scanning dependencies of target _f2py_runtime_library [ 0%] Building C object CMakeFiles/_f2py_runtime_library.dir/usr/lib/python3.8/site-packages/numpy/f2py/src/fortranobject.c.o In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /usr/lib/python3.8/site-packages/numpy/f2py/src/fortranobject.h:13, from /usr/lib/python3.8/site-packages/numpy/f2py/src/fortranobject.c:2: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ [ 0%] Linking C static library lib_f2py_runtime_library.a [ 0%] Built target _f2py_runtime_library [ 0%] Generating _wrappermodule.c, _wrapper-f2pywrappers.f Reading fortran codes... Reading file '/home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/_wrapper.pyf' (format:free) Reading file '/home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/analysis.pyf' (format:free) Reading file '/home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/math.pyf' (format:free) Reading file '/home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/synthesis.pyf' (format:free) Reading file '/home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/transform.pyf' (format:free) Reading file '/home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/_helper.pyf' (format:free) Post-processing... Block: SLYCOT Block: _wrapper Block: ab01nd Block: ab05md Block: ab05nd Block: ab07nd Block: ab08nd Block: ab08nz Block: ab09ad Block: ab09ax Block: ab09bd Block: ab09md Block: ab09nd Block: ab13bd Block: ab13dd Block: ab13ed Block: ab13fd Block: ag08bd Block: mc01td Block: mb03rd Block: mb03vd Block: mb03vy Block: mb03wd Block: mb05md Block: mb05nd Block: sb01bd Block: sb02md Block: sb02od_n Block: sb02od_c Block: sb02od_d Block: sb02od_b Block: sb02mt_n Block: sb02mt_c Block: sb02mt_nl Block: sb02mt_cl Block: sb03md Block: sb03od Block: sb04md Block: sb04qd Block: sb10ad Block: sb10dd Block: sb10fd Block: sb10hd Block: sb10jd Block: sg03ad Block: sg02ad_g Block: sg02ad_bn Block: sg02ad_bc Block: sg02ad_bd Block: sg02ad_bb Block: sg03bd Block: tb01id Block: tb03ad_l Block: tb03ad_r Block: tb04ad_r Block: tb04ad_c Block: tb05ad_ag Block: tb05ad_ng Block: tb05ad_nh Block: tc01od_l Block: tc01od_r Block: tc04ad_l Block: tc04ad_r Block: td04ad_r Block: td04ad_c Block: tf01md Block: tf01rd Block: tb01pd Block: tg01ad Block: tg01fd_nn Block: tg01fd_ii Block: tg01fd_uu Block: ftruefalse Block: xerbla Post-processing (stage 2)... Building modules... Building module "_wrapper"... Constructing wrapper function "ab01nd"... a,b,ncont,indcon,nblk,z,tau,info = ab01nd(jobz,n,m,a,b,[tol,ldwork]) Constructing wrapper function "ab05md"... n,a,b,c,d,info = ab05md(n1,m1,p1,n2,p2,a1,b1,c1,d1,a2,b2,c2,d2,[uplo,ldwork]) Constructing wrapper function "ab05nd"... n,a,b,c,d,controlinfo = ab05nd(n1,m1,p1,n2,alpha,a1,b1,c1,d1,a2,b2,c2,d2,[ldwork]) Constructing wrapper function "ab07nd"... a,b,c,d,rcond,info = ab07nd(n,m,a,b,c,d,[ldwork,overwrite_a,overwrite_b,overwrite_c,overwrite_d]) Constructing wrapper function "ab08nd"... getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' nu,rank_bn,dinfz,nkror,nkrol,infz,kronr,kronl,af,bf,info = ab08nd(n,m,p,a,b,c,d,[equil,tol,ldwork]) Constructing wrapper function "ab08nz"... getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' nu,rank_bn,dinfz,nkror,nkrol,infz,kronr,kronl,af,bf,zwork,info = ab08nz(n,m,p,a,b,c,d,[equil,tol,lzwork]) Constructing wrapper function "ab09ad"... nr,a,b,c,hsv,iwarn,info = ab09ad(dico,job,equil,ordsel,n,m,p,nr,a,b,c,[tol,ldwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "ab09ax"... nr,a,b,c,hsv,t,ti,iwarn,info = ab09ax(dico,job,ordsel,n,m,p,nr,a,b,c,[tol,ldwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "ab09bd"... nr,a,b,c,d,hsv,iwarn,info = ab09bd(dico,job,equil,ordsel,n,m,p,nr,a,b,c,d,[tol1,tol2,ldwork,overwrite_a,overwrite_b,overwrite_c,overwrite_d]) Constructing wrapper function "ab09md"... nr,a,b,c,ns,hsv,iwarn,info = ab09md(dico,job,equil,ordsel,n,m,p,nr,alpha,a,b,c,[tol,ldwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "ab09nd"... nr,a,b,c,d,ns,hsv,iwarn,info = ab09nd(dico,job,equil,ordsel,n,m,p,nr,alpha,a,b,c,d,[tol1,tol2,ldwork,overwrite_a,overwrite_b,overwrite_c,overwrite_d]) Creating wrapper for Fortran function "ab13bd"("ab13bd")... Constructing wrapper function "ab13bd"... ab13bd,nq,iwarn,info = ab13bd(dico,jobn,n,m,p,a,b,c,d,tol) Constructing wrapper function "ab13dd"... fpeak,gpeak,info = ab13dd(dico,jobe,equil,jobd,n,m,p,fpeak,a,e,b,c,d,[tol]) Constructing wrapper function "ab13ed"... low,high,info = ab13ed(n,a,[tol]) Constructing wrapper function "ab13fd"... beta,omega,info = ab13fd(n,a,[tol]) Constructing wrapper function "ag08bd"... a,e,nfz,nrank,niz,dinfz,nkror,ninfe,nkrol,infz,kronr,infe,kronl,info = ag08bd(equil,l,n,m,p,a,e,b,c,d,tol,ldwork,[overwrite_a,overwrite_e,overwrite_b,overwrite_c,overwrite_d]) Constructing wrapper function "mc01td"... dp,stable,nz,iwarn,info = mc01td(dico,dp,p) Constructing wrapper function "mb03rd"... a,x,nblcks,blsize,wr,wi,info = mb03rd(jobx,sort,n,pmax,a,x,tol,[overwrite_a,overwrite_x]) Constructing wrapper function "mb03vd"... a,tau,info = mb03vd(n,ilo,ihi,a,[overwrite_a]) Constructing wrapper function "mb03vy"... a,info = mb03vy(n,ilo,ihi,a,tau,[ldwork,overwrite_a]) Constructing wrapper function "mb03wd"... h,z,wr,wi,info = mb03wd(job,compz,n,ilo,ihi,iloz,ihiz,h,z,[ldwork,overwrite_h,overwrite_z]) Constructing wrapper function "mb05md"... getarrdims:warning: assumed shape array, using 0 instead of '*' a,v,y,valr,vali,info = mb05md(balanc,n,delta,a,[overwrite_a]) Constructing wrapper function "mb05nd"... ex,exint,info = mb05nd(n,delta,a,tol,[overwrite_ex,overwrite_exint]) Constructing wrapper function "sb01bd"... a,wr,wi,nfp,nap,nup,f,z,iwarn,info = sb01bd(dico,n,m,np,alpha,a,b,wr,wi,[tol,ldwork,overwrite_a,overwrite_wr,overwrite_wi]) Constructing wrapper function "sb02md"... a,q,rcond,wr,wi,s,u,info = sb02md(dico,n,a,g,q,[hinv,uplo,scal,sort,ldwork,overwrite_a]) Constructing wrapper function "sb02od_n"... rcond,x,alfar,alfai,beta,s,t,info = sb02od_n(dico,n,m,a,b,q,r,l,[uplo,jobl,sort,tol,ldwork]) Constructing wrapper function "sb02od_c"... rcond,x,alfar,alfai,beta,s,t,info = sb02od_c(dico,n,m,p,a,b,q,r,l,[uplo,jobl,sort,tol,ldwork]) Constructing wrapper function "sb02od_d"... rcond,x,alfar,alfai,beta,s,t,info = sb02od_d(dico,n,m,p,a,b,q,r,l,[uplo,jobl,sort,tol,ldwork]) Constructing wrapper function "sb02od_b"... rcond,x,alfar,alfai,beta,s,t,info = sb02od_b(dico,n,m,p,a,b,q,r,l,[uplo,jobl,sort,tol,ldwork]) Constructing wrapper function "sb02mt_n"... a,b,q,r,l,ipiv,oufact,g,info = sb02mt_n(n,m,b,r,[uplo,ldwork,overwrite_b,overwrite_r]) Constructing wrapper function "sb02mt_c"... a,b,q,r,l,ipiv,oufact,g,info = sb02mt_c(n,m,b,r,[uplo,overwrite_b,overwrite_r]) Constructing wrapper function "sb02mt_nl"... a,b,q,r,l,ipiv,oufact,g,info = sb02mt_nl(n,m,a,b,q,r,l,[uplo,ldwork,overwrite_a,overwrite_b,overwrite_q,overwrite_r,overwrite_l]) Constructing wrapper function "sb02mt_cl"... a,b,q,r,l,ipiv,oufact,g,info = sb02mt_cl(n,m,a,b,q,r,l,[uplo,overwrite_a,overwrite_b,overwrite_q,overwrite_r,overwrite_l]) Constructing wrapper function "sb03md"... c,scale,sep,ferr,wr,wi,info = sb03md(dico,n,c,a,u,[job,fact,trana,ldwork,overwrite_c]) Constructing wrapper function "sb03od"... b,scale,wr,wi,info = sb03od(dico,n,m,a,q,b,[fact,trans,ldwork,overwrite_b]) Constructing wrapper function "sb04md"... a,b,c,z,info = sb04md(n,m,a,b,c,[ldwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "sb04qd"... a,b,c,z,info = sb04qd(n,m,a,b,c,[ldwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "sb10ad"... gamma,ak,bk,ck,dk,ac,bc,cc,dc,rcond,info = sb10ad(job,n,m,np,ncon,nmeas,gamma,a,b,c,d,[gtol,actol,liwork,ldwork]) getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check n>=0)" is mapped to C "int" (to override define dict(integer = dict(check n>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check m>=0)" is mapped to C "int" (to override define dict(integer = dict(check m>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). getctype: "integer(kind=check p>=0)" is mapped to C "int" (to override define dict(integer = dict(check p>=0="<C typespec>")) in /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/.f2py_f2cmap file). Constructing wrapper function "sb10dd"... gamma,ak,bk,ck,dk,x,z,rcond,info = sb10dd(n,m,np,ncon,nmeas,gamma,a,b,c,d,[tol,ldwork]) Constructing wrapper function "sb10fd"... ak,bk,ck,dk,rcond,info = sb10fd(n,m,np,ncon,nmeas,gamma,a,b,c,d,tol,ldwork) Constructing wrapper function "sb10hd"... ak,bk,ck,dk,rcond,info = sb10hd(n,m,np,ncon,nmeas,a,b,c,d,[tol,ldwork]) Constructing wrapper function "sb10jd"... a,b,c,d,nsys,info = sb10jd(n,m,np,a,b,c,d,e,ldwork,[overwrite_a,overwrite_b,overwrite_c,overwrite_d,overwrite_e]) Constructing wrapper function "sg03ad"... a,e,q,z,x,scale,sep,ferr,alphar,alphai,beta,info = sg03ad(dico,job,fact,trans,uplo,n,a,e,q,z,x,[ldwork]) Constructing wrapper function "sg02ad_g"... rcondu,x,alfar,alfai,beta,s,t,u,iwarn,info = sg02ad_g(dico,uplo,sort,acc,n,a,e,b,q,[ldwork]) Constructing wrapper function "sg02ad_bn"... rcondu,x,alfar,alfai,beta,s,t,u,iwarn,info = sg02ad_bn(dico,uplo,jobl,scal,sort,acc,n,m,a,e,b,q,r,l,[tol,ldwork]) Constructing wrapper function "sg02ad_bc"... rcondu,x,alfar,alfai,beta,s,t,u,iwarn,info = sg02ad_bc(dico,jobl,scal,sort,acc,n,m,p,a,e,b,q,r,l,[tol,ldwork]) Constructing wrapper function "sg02ad_bd"... rcondu,x,alfar,alfai,beta,s,t,u,iwarn,info = sg02ad_bd(dico,jobl,scal,sort,acc,n,m,p,a,e,b,q,r,l,[tol,ldwork]) Constructing wrapper function "sg02ad_bb"... rcondu,x,alfar,alfai,beta,s,t,u,iwarn,info = sg02ad_bb(dico,jobl,scal,sort,acc,n,m,p,a,e,b,q,r,l,[tol,ldwork]) Constructing wrapper function "sg03bd"... b,scale,alphar,alphai,beta,info = sg03bd(dico,n,m,a,e,q,z,b,[fact,trans,ldwork,overwrite_b]) Constructing wrapper function "tb01id"... maxred,a,b,c,scale,info = tb01id(n,m,p,maxred,a,b,c,[job,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "tb03ad_l"... a,b,c,nr,index_bn,pcoeff,qcoeff,vcoeff,info = tb03ad_l(n,m,p,a,b,c,d,[equil,tol,ldwork]) Constructing wrapper function "tb03ad_r"... a,b,c,nr,index_bn,pcoeff,qcoeff,vcoeff,info = tb03ad_r(n,m,p,a,b,c,d,[equil,tol,ldwork]) Constructing wrapper function "tb04ad_r"... a,b,c,nr,index_bn,dcoeff,ucoeff,info = tb04ad_r(n,m,p,a,b,c,d,[tol1,tol2,ldwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "tb04ad_c"... a,b,c,nr,index_bn,dcoeff,ucoeff,info = tb04ad_c(n,m,p,a,b,c,d,[tol1,tol2,ldwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "tb05ad_ag"... a,b,c,rcond,g,evre,evim,hinvb,info = tb05ad_ag(n,m,p,freq,a,b,c,[ldwork,lzwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "tb05ad_ng"... a,b,c,g,hinvb,info = tb05ad_ng(n,m,p,freq,a,b,c,[ldwork,lzwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "tb05ad_nh"... g,hinvb,info = tb05ad_nh(n,m,p,freq,a,b,c,[ldwork,lzwork]) Constructing wrapper function "tc01od_l"... pcoeff,qcoeff,info = tc01od_l(m,p,indlim,pcoeff,qcoeff) Constructing wrapper function "tc01od_r"... info = tc01od_r(p,indlim,pcoeff,qcoeff,[m]) Constructing wrapper function "tc04ad_l"... getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' n,rcond,a,b,c,d,info = tc04ad_l(m,p,index_bn,pcoeff,qcoeff,n,[ldwork]) Constructing wrapper function "tc04ad_r"... getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' n,rcond,a,b,c,d,info = tc04ad_r(m,p,index_bn,pcoeff,qcoeff,n,[ldwork]) Constructing wrapper function "td04ad_r"... getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' nr,a,b,c,d,info = td04ad_r(m,p,index_bn,dcoeff,ucoeff,nr,[tol,ldwork,overwrite_dcoeff,overwrite_ucoeff]) Constructing wrapper function "td04ad_c"... getarrdims:warning: assumed shape array, using 0 instead of '*' getarrdims:warning: assumed shape array, using 0 instead of '*' nr,a,b,c,d,info = td04ad_c(m,p,index_bn,dcoeff,ucoeff,nr,[tol,ldwork,overwrite_dcoeff,overwrite_ucoeff]) Constructing wrapper function "tf01md"... x,y,info = tf01md(n,m,p,ny,a,b,c,d,u,x,[overwrite_x]) Constructing wrapper function "tf01rd"... h,info = tf01rd(na,nb,nc,n,a,b,c,[ldwork]) Constructing wrapper function "tb01pd"... a,b,c,nr,info = tb01pd(n,m,p,a,b,c,[job,equil,tol,ldwork,overwrite_a,overwrite_b,overwrite_c]) Constructing wrapper function "tg01ad"... a,e,b,c,lscale,rscale,info = tg01ad(job,l,n,m,p,thresh,a,e,b,c,[overwrite_a,overwrite_e,overwrite_b,overwrite_c]) Constructing wrapper function "tg01fd_nn"... a,e,b,c,ranke,rnka22,info = tg01fd_nn(joba,l,n,m,p,a,e,b,c,tol,ldwork,[overwrite_a,overwrite_e,overwrite_b,overwrite_c]) Constructing wrapper function "tg01fd_ii"... a,e,b,c,q,z,ranke,rnka22,info = tg01fd_ii(joba,l,n,m,p,a,e,b,c,tol,ldwork,[overwrite_a,overwrite_e,overwrite_b,overwrite_c]) Constructing wrapper function "tg01fd_uu"... a,e,b,c,q,z,ranke,rnka22,info = tg01fd_uu(joba,l,n,m,p,a,e,b,c,q,z,tol,ldwork,[overwrite_a,overwrite_e,overwrite_b,overwrite_c,overwrite_q,overwrite_z]) Constructing wrapper function "ftruefalse"... ftrue,ffalse = ftruefalse() Constructing wrapper function "xerbla"... xerbla(srname,info) Wrote C/API module "_wrapper" to file "./_wrappermodule.c" Fortran 77 wrappers are saved to "./_wrapper-f2pywrappers.f" Building module "SLYCOT"... Wrote C/API module "SLYCOT" to file "./SLYCOTmodule.c" Scanning dependencies of target _wrapper [ 0%] Building C object slycot/CMakeFiles/_wrapper.dir/_wrappermodule.c.o In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /usr/lib/python3.8/site-packages/numpy/f2py/src/fortranobject.h:13, from /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build/slycot/_wrappermodule.c:16: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ [ 1%] Building C object slycot/CMakeFiles/_wrapper.dir/usr/lib/python3.8/site-packages/numpy/f2py/src/fortranobject.c.o In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /usr/lib/python3.8/site-packages/numpy/f2py/src/fortranobject.h:13, from /usr/lib/python3.8/site-packages/numpy/f2py/src/fortranobject.c:2: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ [ 1%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/_wrapper-f2pywrappers.f.o [ 1%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/AB01MD.f.o [ 1%] Building Fortran object 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slycot/CMakeFiles/_wrapper.dir/src/IB01CD.f.o [ 18%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01MD.f.o [ 18%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01MY.f.o [ 18%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01ND.f.o [ 18%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01OD.f.o [ 18%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01OY.f.o [ 19%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01PD.f.o [ 19%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01PX.f.o [ 19%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01PY.f.o [ 19%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01QD.f.o [ 20%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB01RD.f.o [ 20%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB03AD.f.o [ 20%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/IB03BD.f.o [ 20%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA01AD.f.o [ 20%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02AD.f.o [ 21%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02BD.f.o [ 21%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02BZ.f.o [ 21%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02CD.f.o [ 21%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02CZ.f.o [ 21%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02DD.f.o [ 22%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02ED.f.o [ 22%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02FD.f.o [ 22%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02GD.f.o [ 22%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02HD.f.o [ 22%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02ID.f.o /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/MA02ID.f:188:21: 184 | DO 90 J = 1, N+1 | 2 ...... 188 | DWORK(J-1) = DWORK(J-1) + TEMP | 1 Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2) /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/MA02ID.f:188:34: 184 | DO 90 J = 1, N+1 | 2 ...... 188 | DWORK(J-1) = DWORK(J-1) + TEMP | 1 Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2) /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/MA02ID.f:230:21: 226 | DO 160 J = 1, N+1 | 2 ...... 230 | DWORK(J-1) = DWORK(J-1) + TEMP | 1 Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2) /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/slycot/src/MA02ID.f:230:34: 226 | DO 160 J = 1, N+1 | 2 ...... 230 | DWORK(J-1) = DWORK(J-1) + TEMP | 1 Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2) [ 23%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MA02JD.f.o [ 23%] Building Fortran object slycot/CMakeFiles/_wrapper.dir/src/MB01MD.f.o [ 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/home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/examples.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/exceptions.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/analysis.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/math.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/synthesis.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/transform.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/version.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/__init__.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_ab01.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_ab08n.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_ag08bd.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_examples.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_exceptions.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_mb.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_mc.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_sb.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_analysis.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_transform.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_sg02ad.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_sg03ad.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_tb05ad.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_td04ad.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_tg01ad.py -- Installing: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_tg01fd.py -------------------------------------------------------------------------------- -- Trying "Unix Makefiles" generator -------------------------------- --------------------------- ---------------------- ----------------- ------------ ------- -- -- ------- ------------ ----------------- ---------------------- --------------------------- -------------------------------- -- Trying "Unix Makefiles" generator - success -------------------------------------------------------------------------------- Configuring Project Working directory: /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-build Command: cmake /home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0 -G 'Unix Makefiles' -DCMAKE_INSTALL_PREFIX:PATH=/home/acxz/.cache/yay/python-slycot/src/slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/cmake-install -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python -DPYTHON_VERSION_STRING:STRING=3.8.5 -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.8 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/libpython3.8.so -DSKBUILD:BOOL=TRUE -DCMAKE_MODULE_PATH:PATH=/usr/lib/python3.8/site-packages/skbuild/resources/cmake -DSLYCOT_VERSION:STRING=0.4.0 -DGIT_REVISION:STRING=ac0944b363a6cfcc0c3d5128cdd484d74173aa3b -DISRELEASE:STRING=True -DFULL_VERSION=0.4.0.gitac0944b -DCMAKE_BUILD_TYPE:STRING=Release running build running build_py creating _skbuild/linux-x86_64-3.8/setuptools/lib creating _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/__init__.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/exceptions.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/analysis.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/examples.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/synthesis.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/version.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/transform.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/math.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot creating _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/__init__.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_sb.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_sg02ad.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_transform.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_tb05ad.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_exceptions.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_tg01ad.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_ab01.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_analysis.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_mb.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_sg03ad.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_examples.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_mc.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_td04ad.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_tg01fd.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_ab08n.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/tests/test_ag08bd.py -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests copying _skbuild/linux-x86_64-3.8/cmake-install/slycot/_wrapper.cpython-38-x86_64-linux-gnu.so -> _skbuild/linux-x86_64-3.8/setuptools/lib/slycot copied 25 files running build_ext ==> Starting check()... ============================= test session starts ============================== platform linux -- Python 3.8.5, pytest-6.1.0, py-1.9.0, pluggy-0.13.1 rootdir: /home/acxz/.cache/yay/python-slycot/src collected 108 items slycot-0.4.0.0/_skbuild/linux-x86_64-3.8/setuptools/lib/slycot/tests/test_ab01.py ==> ERROR: A failure occurred in check(). Aborting... error making: python-slycotpip is building your slycot wheel from source. Please use
pip -vorpip --log piplog.logto see which library it builds against.pip install slycot -v:You have to clear your pip cache first
Now there is also an arch package built against MKL from
https://download.opensuse.org/repositories/home:/bnavigator:/archlinux/Arch/x86_64/python-slycot-mkl-0.4.0.0-1-x86_64.pkg.tar.zstI installed it on my Archlinux machine together with
python-{scipy,numpy}-mkl-binfrom AUR and the unit tests (pytest --pyargs slycot) pass. 🎉- changed the title
[-]test_ab01.py fails when intel-mkl is installed[/-][+]Archlinux: Slycot compiled against MKL crashes[/+]on Oct 2, 2020 You have to clear your pip cache first
ah my bad I have updated the gist: https://gist.github.com/acxz/9f52adbc843bb4d6da538ffa5a518cf9
Now there is also an arch package built against MKL
Sweet! I prob won't use it unless its on the AUR tho..
That log is still garbage. Have you even tried to look into it?
I can only reiterate what is written all over the Arch wiki: If you don't know how to build your own package from a PKGBUILD, you should not use AUR either. Anyway here is the AUR package: https://aur.archlinux.org/packages/python-slycot-mkl/
That log is still garbage. Have you even tried to look into it?
Ah once again sorry about that. I should have been more specific. The relevant content is near the bottom. You need to view the entire file not just the preview on gist. Here is the link for easy access. https://gist.githubusercontent.com/acxz/9f52adbc843bb4d6da538ffa5a518cf9/raw/a13e11997576cd2221a4ecaf49138d1bbfe15c9b/slycot-pip-install-no-cache.txt
Thx for creating the AUR package,
Yeah you are right maybe I shouldn't be using the AUR...Hmm, now I see that you are the maintainer of >500 packages in AUR. Honestly, I am surprised you are not able to provide the relevant information right away, not to mention the misuse of the out-of-date flag.
So your pip build finds the same MKL as your yay/AUR build. It does not run the unit tests. But does the pip package actually work? What does
pytest --pyargs slycot -vsay?pytest --pyargs slycot -v====================================================== test session starts ======================================================= platform linux -- Python 3.8.5, pytest-6.1.0, py-1.9.0, pluggy-0.13.1 -- /usr/bin/python cachedir: .pytest_cache rootdir: /home/acxz collected 108 items tests/test_ab01.py::test_ab01nd %A crash. Pip package won't help you then.
Reacted by Akash PatelBy default, the build still finds and builds against openblas, not MKL.
hmm weird that doesn't seem to be happening for me.
Okay, now my default package also finds MKL. Maybe the environment was not reloaded on my first tries.
If you compile against a specific BLAS/LAPACK implementation, your whole ecosystem including numpy and scipy need to be linked to the same implementation. This is highly distribution specific. When mixing package repositories (conda, pip wheels, official distribution, additional repositories like AUR, custom PPAs, ...) chances are high that the packages are incompatible because they link to different implementations.
OTOH, if you link against an installed reference NetLIB BLAS/LAPACK implementation (
BLA_VENDOR=Generic) the resulting library should work with any ABI compatible implementation as long as the other libraries do the same. Some Linux distributions do this and allow the system administrator to switch via e.g. update-alternatives [1, 2] or eselect. There is also FlexiBLAS which provides a runtime switching layer. Fedora seems to use this or at least considers to do it. AUR has a flexiblas package and an ATLAS package based on it.I could not find any guidelines for Archlinux packaging. The python-numpy packages has
depends=('blas')andoptdepends=('openblas'), and the binary package in Extra is linked against the generic library name libblas.so.3 which is provided byblas(NetLIB) oropenblas(but notintel-mkl)Tl;dr: Link all your libraries against the same LAPACK/BLAS implementation.
For your specific case, you have several options:
Force the link against the same implementation as the official numpy and scipy packages throughUse updated AUR python-slycot which enforcesBLA_VENDOR=Generic makepkg python-slycotBLA_VENDOR=Generictogether with the official Archlinux numpy and scipy packages- Use python-numpy-mkl and python-scipy-mkl (specified as depends in python-slycot-mkl)
- Find out why
intel-mkldoes not provide libblas.so (et al) and file a bug against intel-mkl package if it should be there.
Reacted by Akash PatelClosing, as we cannot do anything about this "upstream". If anyone thinks otherwise, please comment or open a new issue/PR with your proposal.
thx for getting down to the bottom of this @bnavigator !
When running the test suite,
test_ab01.pyfails for me with the following error:Specifically:
If I compile and run the test_suite without intel-mkl on my system the test_suite runs successfully.
System:
Version: 0.4.0
OS: ArchLinux
Intel-MKL: 2020.2.254
Python: 3.8.5
Let me know if I can give more information.