[petsc-users] configure error

Junchao Zhang junchao.zhang at gmail.com
Sat May 15 20:44:59 CDT 2021 

Add --show to the failing nvcc_wrapper command and see how nvcc_wrapper
parses the options

PATH=/global/common/sw/cray/sles15/x86_64/zlib/1.2.11/gcc/8.2.0/pep2pal/bin:/global/common/sw/cray/cnl7/haswell/cmake/3.18.2/bin:/opt/cray/rca/2.2.20-7.0.1.1_4.62__g8e3fb5b.ari/bin:/opt/cray/alps/6.6.58-7.0.1.1_6.20__g437d88db.ari/sbin:/opt/cray/alps/default/bin:/opt/cray/job/2.2.4-7.0.1.1_3.48__g36b56f4.ari/bin:/opt/cray/pe/craype/2.6.2/bin:/usr/common/software/sles15_cgpu/openmpi/4.0.3/gcc/bin:/usr/common/software/sles15_cgpu/hpcsdk/20.11/Linux_x86_64/20.11/compilers/bin:/usr/common/software/sles15_cgpu/hpcsdk/20.11/Linux_x86_64/20.11/cuda/bin:/usr/common/software/sles15_cgpu/cuda/11.1.1/bin:/usr/common/software/sles15_cgpu/gcc/8.3.0/bin:/opt/esslurm/bin:/opt/cray/pe/modules/
3.2.11.4/bin:/usr/common/software/bin:/usr/common/nsg/bin:/opt/ovis/bin:/opt/ovis/sbin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/cray/pe/bin:`dirname
<http://3.2.11.4/bin:/usr/common/software/bin:/usr/common/nsg/bin:/opt/ovis/bin:/opt/ovis/sbin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/cray/pe/bin:dirname>
/usr/common/software/sles15_cgpu/cuda/11.1.1/bin/nvcc`
NVCC_WRAPPER_DEFAULT_COMPILER=/usr/common/software/sles15_cgpu/openmpi/4.0.3/gcc/bin/mpicxx
/global/homes/m/madams/petsc/arch-cori-gpu-opt-kokkos-gcc/bin/nvcc_wrapper
--expt-extended-lambda -c -arch=sm_70 -Xcompiler -rdynamic -DLANDAU_DIM=2
-DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC -DLANDAU_MAX_Q=4
-Xcompiler -fPIC -O3  -gencode arch=compute_80,code=sm_80
 -I/usr/common/software/sles15_cgpu/openmpi/4.0.3/gcc/include
-Wno-deprecated-gpu-targets   -I/global/homes/m/madams/petsc/include
-I/global/homes/m/madams/petsc/arch-cori-gpu-opt-kokkos-gcc/include
-I/usr/common/software/sles15_cgpu/openmpi/4.0.3/gcc/include
-I/usr/common/software/sles15_cgpu/cuda/11.1.1/include
 /global/u2/m/madams/petsc/src/sys/objects/kokkos/kinit.kokkos.cxx -o
arch-cori-gpu-opt-kokkos-gcc/obj/sys/objects/kokkos/kinit.o --show

--Junchao Zhang


On Sat, May 15, 2021 at 7:14 PM Mark Adams <mfadams at lbl.gov> wrote:

> Thanks,
> Now I get an error in make all. THis was working a few weeks ago.
> Make.log was empty but here is the output.
>  ....
>        CC arch-cori-gpu-opt-kokkos-gcc/obj/sys/error/ftn-custom/zerrf.o
>           CC arch-cori-gpu-opt-kokkos-gcc/obj/sys/f90-src/f90_cwrap.o
>           CC arch-cori-gpu-opt-kokkos-gcc/obj/vec/is/utils/hdf5io.o
>
> PATH=/global/common/sw/cray/sles15/x86_64/zlib/1.2.11/gcc/8.2.0/pep2pal/bin:/global/common/sw/cray/cnl7/haswell/cmake/3.18.2/bin:/opt/cray/rca/2.2.20-7.0.1.1_4.62__g8e3fb5b.ari/bin:/opt/cray/alps/6.6.58-7.0.1.1_6.20__g437d88db.ari/sbin:/opt/cray/alps/default/bin:/opt/cray/job/2.2.4-7.0.1.1_3.48__g36b56f4.ari/bin:/opt/cray/pe/craype/2.6.2/bin:/usr/common/software/sles15_cgpu/openmpi/4.0.3/gcc/bin:/usr/common/software/sles15_cgpu/hpcsdk/20.11/Linux_x86_64/20.11/compilers/bin:/usr/common/software/sles15_cgpu/hpcsdk/20.11/Linux_x86_64/20.11/cuda/bin:/usr/common/software/sles15_cgpu/cuda/11.1.1/bin:/usr/common/software/sles15_cgpu/gcc/8.3.0/bin:/opt/esslurm/bin:/opt/cray/pe/modules/
> 3.2.11.4/bin:/usr/common/software/bin:/usr/common/nsg/bin:/opt/ovis/bin:/opt/ovis/sbin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/cray/pe/bin:`dirname
> <http://3.2.11.4/bin:/usr/common/software/bin:/usr/common/nsg/bin:/opt/ovis/bin:/opt/ovis/sbin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/cray/pe/bin:dirname>
> /usr/common/software/sles15_cgpu/cuda/11.1.1/bin/nvcc`
> NVCC_WRAPPER_DEFAULT_COMPILER=/usr/common/software/sles15_cgpu/openmpi/4.0.3/gcc/bin/mpicxx
> /global/homes/m/madams/petsc/arch-cori-gpu-opt-kokkos-gcc/bin/nvcc_wrapper
> --expt-extended-lambda -c -arch=sm_70 -Xcompiler -rdynamic -DLANDAU_DIM=2
> -DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC -DLANDAU_MAX_Q=4
> -Xcompiler -fPIC -O3  -gencode arch=compute_80,code=sm_80
>  -I/usr/common/software/sles15_cgpu/openmpi/4.0.3/gcc/include
> -Wno-deprecated-gpu-targets   -I/global/homes/m/madams/petsc/include
> -I/global/homes/m/madams/petsc/arch-cori-gpu-opt-kokkos-gcc/include
> -I/usr/common/software/sles15_cgpu/openmpi/4.0.3/gcc/include
> -I/usr/common/software/sles15_cgpu/cuda/11.1.1/include
>  /global/u2/m/madams/petsc/src/sys/objects/kokkos/kinit.kokkos.cxx -o
> arch-cori-gpu-opt-kokkos-gcc/obj/sys/objects/kokkos/kinit.o
> g++: error: arch=compute_80: No such file or directory
> g++: error: code=sm_80: No such file or directory
> gmake[3]: *** [gmakefile:188:
> arch-cori-gpu-opt-kokkos-gcc/obj/sys/objects/kokkos/kinit.o] Error 1
> gmake[3]: *** Waiting for unfinished jobs....
>           CC arch-cori-gpu-opt-kokkos-gcc/obj/vec/is/utils/isio.o
>           CC arch-cori-gpu-opt-kokkos-gcc/obj/vec/is/utils/ftn-auto/pmapf.o
>           CC arch-cori-gpu-opt-kokkos-gcc/obj/vec/is/utils/pmap.o
>           CC arch-cori-gpu-opt-kokkos-gcc/obj/vec/is/utils/psort.o
>           CC arch-cori-gpu-opt-kokkos-gcc/obj/vec/is/utils/isltog.o
>           FC arch-cori-gpu-opt-kokkos-gcc/obj/vec/f90-mod/petscvecmod.o
>        CUDAC arch-cori-gpu-opt-kokkos-gcc/obj/sys/memory/cuda/mcudahost.o
>    CUDAC.dep arch-cori-gpu-opt-kokkos-gcc/obj/sys/memory/cuda/mcudahost.o
> gmake[2]: *** [/global/homes/m/madams/petsc/lib/petsc/conf/rules:50: libs]
> Error 2
> **************************ERROR*************************************
>   Error during compile, check
> arch-cori-gpu-opt-kokkos-gcc/lib/petsc/conf/make.log
>   Send it and arch-cori-gpu-opt-kokkos-gcc/lib/petsc/conf/configure.log to
> petsc-maint at mcs.anl.gov
> ********************************************************************
> gmake[1]: *** [makefile:40: all] Error 1
> make: *** [GNUmakefile:9: all] Error 2
>
> On Sat, May 15, 2021 at 5:30 PM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>>   Bitbucket is off-line. Do you need fortran stubs at this moment? If not
>> use  --with-fortran-interface=0
>>
>>
>> On May 15, 2021, at 2:51 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>
>> I can build a non-kokkos PETSc here (Cori/GPU) but I get this error with
>> Kokkos.
>> Any suggestions?
>> Thanks,
>> Mark
>>
>> =============================================================================================
>>
>>
>>
>> =============================================================================================
>>
>>
>>                                                                 Trying to
>> download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING
>>
>>
>>
>>  =============================================================================================
>>
>>
>>
>> =============================================================================================
>>
>>
>>                                                                 Trying to
>> download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING
>>
>>
>>
>>  =============================================================================================
>>
>>
>>
>> =============================================================================================
>>
>>
>>                                                                 Trying to
>> download https://bitbucket.org/petsc/pkg-sowing/get/v1.1.26-p1.tar.gz
>> for SOWING
>>
>>
>>  =============================================================================================
>>
>>
>>
>>
>>
>>
>>
>> *******************************************************************************
>>          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
>> details):
>>
>> -------------------------------------------------------------------------------
>> Error during download/extract/detection of SOWING:
>> Unable to clone sowing
>> Could not execute "['git clone https://bitbucket.org/petsc/pkg-sowing.git
>> /global/u2/m/madams/petsc/arch-cori-gpu-opt-kokkos-gcc/externalpackages/git.sowing']":
>> Cloning into
>> '/global/u2/m/madams/petsc/arch-cori-gpu-opt-kokkos-gcc/externalpackages/git.sowing'...
>> fatal: unable to access 'https://bitbucket.org/petsc/pkg-sowing.git/':
>> The requested URL returned error: 503
>> Unable to download package SOWING from: git://
>> https://bitbucket.org/petsc/pkg-sowing.git
>> * If URL specified manually - perhaps there is a typo?
>> * If your network is disconnected - please reconnect and rerun ./configure
>> * Or perhaps you have a firewall blocking the download
>> * You can run with --with-packages-download-dir=/adirectory and
>> ./configure will instruct you what packages to download manually
>> * or you can download the above URL manually, to /yourselectedlocation
>>   and use the configure option:
>>   --download-sowing=/yourselectedlocation
>>     Unable to clone sowing
>> Could not execute "['git clone https://bitbucket.org/petsc/pkg-sowing.git
>> /global/u2/m/madams/petsc/arch-cori-gpu-opt-kokkos-gcc/externalpackages/git.sowing']":
>> Cloning into
>> '/global/u2/m/madams/petsc/arch-cori-gpu-opt-kokkos-gcc/externalpackages/git.sowing'...
>> fatal: unable to access 'https://bitbucket.org/petsc/pkg-sowing.git/':
>> The requested URL returned error: 503
>> Unable to download package SOWING from: git://
>> https://bitbucket.org/petsc/pkg-sowing.git
>> * If URL specified manually - perhaps there is a typo?
>> * If your network is disconnected - please reconnect and rerun ./configure
>> * Or perhaps you have a firewall blocking the download
>> * You can run with --with-packages-download-dir=/adirectory and
>> ./configure will instruct you what packages to download manually
>> * or you can download the above URL manually, to /yourselectedlocation
>>   and use the configure option:
>>   --download-sowing=/yourselectedlocation
>>     file could not be opened successfully
>> Downloaded package SOWING from:
>> https://bitbucket.org/petsc/pkg-sowing/get/v1.1.26-p1.tar.gz is not a
>> tarball.
>> [or installed python cannot process compressed files]
>> * If you are behind a firewall - please fix your proxy and rerun
>> ./configure
>>   For example at LANL you may need to set the environmental variable
>> http_proxy (or HTTP_PROXY?) to  http://proxyout.lanl.gov
>> * You can run with --with-packages-download-dir=/adirectory and
>> ./configure will instruct you what packages to download manually
>> * or you can download the above URL manually, to
>> /yourselectedlocation/v1.1.26-p1.tar.gz
>>   and use the configure option:
>>   --download-sowing=/yourselectedlocation/v1.1.26-p1.tar.gz
>>
>> *******************************************************************************
>> <configure.log>
>>
>>
>>
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