[petsc-users] [Ext] Re: configure error
Kun Jiao
KJiao at slb.com
Mon Jun 15 12:45:15 CDT 2020
I see. Thanks.
We are computing everything on float. Therefore I choose --with-precision=single.
Regards,
Kun
Schlumberger-Private
-----Original Message-----
From: Satish Balay <balay at mcs.anl.gov>
Sent: Monday, June 15, 2020 12:40 PM
To: Kun Jiao <KJiao at slb.com>
Cc: Barry Smith <bsmith at petsc.dev>; petsc-users at mcs.anl.gov
Subject: Re: [petsc-users] [Ext] Re: configure error
You need regular MKL. ILP64 can be used with --with-64-bit-blas-indices option.
Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --configModules=PETSc.Configure --optionsModule=config.compilerOptions --configModules=PETSc.Configure --optionsModule=config.compilerOptions PETSC_ARCH=linux-gnu-intel --with-precision=single --with-cc=icc --with-cxx=icc --with-fc=ifort --with-mpi-include=/opt/openmpi_4.0.3_intel2019.3/include --with-mpi-lib="-L/opt/openmpi_4.0.3_intel2019.3/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi" --with-blaslapack-include=/mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl/include --with-blaslapack-lib="-L/mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64 -Wl, --no-as-needed -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" --with-scalapack-lib="-L/mnt/disks/intel-2018-3-222-blade-runtime-e
nv-2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" --with-scalapack-include=/mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl/include --with-cmake=1 --prefix=/opt/petsc_3.10.4_intel2019.3 --known-endian=big --with-debugging=0 --COPTFLAGS=" -Ofast -xHost" --CXXOPTFLAGS=" -Ofast -xHost" --FOPTLAGS=" -Ofast -xHost" --with-x=0 --with-64-bit-indices
This is a complicated build command. What are you trying to do?
> --with-precision=single
Are you sure this is what you want?
> --with-scalapack-lib=
PETSc does not use scalapack. Its a dependency for MUMPS
[apart from the mixing MPI issue]
Its best to use appropriate mpicc etc wrappers so that one doesn't files from multiple MPIs..
And its probably better to use:
--with-blaslapack-dir=/mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl
Satish
On Mon, 15 Jun 2020, Kun Jiao via petsc-users wrote:
> Actually, that is a question I should ask. When I use --with-64-bit-indices option to config petsc, do I need to use 64 integer option in mkl which means -lmkl_intel_ilp64, or I can use 32integer option for mkl which is -lmkl_intel_lp64?
>
>
>
> Schlumberger-Private
> From: Barry Smith <bsmith at petsc.dev>
> Sent: Monday, June 15, 2020 12:29 PM
> To: Kun Jiao <KJiao at slb.com>
> Cc: petsc-users at mcs.anl.gov
> Subject: [Ext] Re: [petsc-users] configure error
>
>
> It is reporting
>
> ld: cannot find -lmkl_intel_ilp64
>
> Please send the output from
>
> ls
> /mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-132838
> /2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl
> ls
> /mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-132838
> /2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib
> ls
> /mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-132838
> /2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64
>
> Also you are mixing using the Intel MPI and OpenMPI, I am not sure this will work.
>
> /opt/openmpi_4.0.3_intel2019.3/lib
> -lmkl_blacs_intelmpi_lp64
>
>
>
>
> On Jun 15, 2020, at 12:11 PM, Kun Jiao via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
>
> Hi,
>
> Lately I run into a configure error with intel
> compiler+openmpi+lapack,
>
> Error message as:
> =============================================================================== TESTING: checkLib from config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:114) *******************************************************************************
> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
> ----------------------------------------------------------------------
> --------- You set a value for --with-blaslapack-lib=<lib>, but
> ['-L/mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-13
> 2838/2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/int
> el64', '-Wl,', '--no-as-needed', '-lmkl_intel_ilp64',
> '-lmkl_intel_thread', '-lmkl_core', '-liomp5', '-lpthread', '-lm',
> '-ldl'] cannot be used
> **********************************************************************
> *********
>
>
> Here is my configure parameters:
>
> ./configure --configModules=PETSc.Configure
> --optionsModule=config.compilerOptions --configModules=PETSc.Configure
> --optionsModule=config.compilerOptions PETSC_ARCH=linux-gnu-intel
> --with-precision=single --with-cc=icc --with-cxx=icc --with-fc=ifort
> --with-mpi-include=/opt/openmpi_4.0.3_intel2019.3/include
> --with-mpi-lib="-L/opt/openmpi_4.0.3_intel2019.3/lib -lmpi_usempif08
> -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi"
> --with-blaslapack-include="/mnt/disks/intel-2018-3-222-blade-runtime-e
> nv-2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.
> 3.199/linux/mkl/include"
> --with-blaslapack-lib="-L/mnt/disks/intel-2018-3-222-blade-runtime-env
> -2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.3.
> 199/linux/mkl/lib/intel64 -Wl, --no-as-needed -lmkl_intel_ilp64
> -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl"
> --with-scalapack-lib="-L/mnt/disks/intel-2018-3-222-blade-runtime-env-
> 2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.3.1
> 9
9/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" --with-scalapack-include=/mnt/disks/intel-2018-3-222-blade-runtime-env-2018-1-07-08-2018-132838/2019.3/intel/compilers_and_libraries_2019.3.199/linux/mkl/include --with-cmake=1 --prefix=/opt/petsc_3.10.4_intel2019.3 --known-endian=big --with-debugging=0 --COPTFLAGS=" -Ofast -xHost" --CXXOPTFLAGS=" -Ofast -xHost" --FOPTLAGS=" -Ofast -xHost" --with-x=0 --with-64-bit-indices
>
> And configure.log attached.
>
> Any suggestion will be great?
>
> Regards,
> Kun
>
>
> Schlumberger-Private
> <configure.log>
>
>
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