Fwd: [pflotran-users: 7076] Fwd: Installation Errors: Setup on Windows 10/Ubuntu/NVIDIA GPU

[PEGGY NGUYEN]

Thanks, Glenn. Here is my configuration log:

Executing: uname -s
stdout: Linux
=============================================================================================
                         Configuring PETSc to compile on your system
=============================================================================================

================================================================================
================================================================================
Starting configure run at Tue, 30 May 2023 09:14:26 -0700
Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --CFLAGS=-O3 --CXXFLAGS=-O3 --FFLAGS=-O3 --with-debugging=no --download-mpich=yes --download-hdf5=yes --with-hdf5-fortran-bindings=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes
Working directory: /home/pnguyen7/petsc
Machine platform:
uname_result(system='Linux', node='DESKTOP-D85JDDR', release='5.15.90.1-microsoft-standard-WSL2', version='#1 SMP Fri Jan 27 02:56:13 UTC 2023', machine='x86_64')
Python version:
3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]
================================================================================
  Environmental variables
SHELL=/bin/bash
WSL2_GUI_APPS_ENABLED=1
WSL_DISTRO_NAME=Ubuntu
NAME=DESKTOP-D85JDDR
PWD=/home/pnguyen7/petsc
LOGNAME=pnguyen7
HOME=/home/pnguyen7
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/570_interop
"configure.log" 19552L, 1270394B

---------- Forwarded message ---------
From: 'Hammond, Glenn E' via pflotran-users <pflotra...@googlegroups.com>
Date: Tue, May 30, 2023 at 8:07 AM
Subject: RE: [pflotran-users: 7076] Fwd: Installation Errors: Setup on Windows 10/Ubuntu/NVIDIA GPU
To: pflotra...@googlegroups.com <pflotra...@googlegroups.com>

Peggy,

 

Please send the configure.log file to pflotr...@googlegroups.com, and we will continue the discussion over there. The log files are often too large for pflotran-users (don’t want to spam everyone). Since this is a PETSc configuration issues, it is likely that you will need to reach out to the PETSc developers, but we can at least provide some input.

 

Glenn

 

From: pflotra...@googlegroups.com <pflotra...@googlegroups.com> On Behalf Of PEGGY NGUYEN
Sent: Monday, May 29, 2023 11:04 PM
To: pflotra...@googlegroups.com
Cc: Margit Maple <margi...@gmail.com>
Subject: Re: [pflotran-users: 7074] Fwd: Installation Errors: Setup on Windows 10/Ubuntu/NVIDIA GPU

 

Hi, Glenn,

 

Thanks for your quick response. Here are the results of using that configuration script:

 

pnguyen7@DESKTOP-D85JDDR:~/petsc$ ./configure --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --download-mpich=yes --download-hdf5=yes --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes
=============================================================================================
                         Configuring PETSc to compile on your system
=============================================================================================
=============================================================================================
                   Running configure on HDF5; this may take several minutes
=============================================================================================

*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
Error running configure on HDF5
*******************************************************************************

 

Thank you,

 

Peggy

 

 

 

 

 

 

On Mon, May 29, 2023 at 10:45 PM 'Hammond, Glenn E' via pflotran-users <pflotra...@googlegroups.com> wrote:

Peggy,

 

What happens when you configure PETSc with:

 

./configure --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --download-mpich=yes --download-hdf5=yes --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes

 

Note that the above has the two *required* command line arguments for HDF5.

 

Glenn

 

From: pflotra...@googlegroups.com <pflotra...@googlegroups.com> On Behalf Of PEGGY NGUYEN
Sent: Monday, May 29, 2023 10:08 PM
To: pflotra...@googlegroups.com
Cc: Margit Maple <margi...@gmail.com>
Subject: [pflotran-users: 7071] Fwd: Installation Errors: Setup on Windows 10/Ubuntu/NVIDIA GPU

 

Check twice before you click! This email originated from outside PNNL.

 

 

---------- Forwarded message ---------
From: PEGGY NGUYEN <pngu...@ucla.edu>
Date: Mon, May 29, 2023 at 10:06 PM
Subject: Installation Errors: Setup on Windows 10/Ubuntu/NVIDIA GPU
To: <flotra...@googlegroups.com>
Cc: Margit Maple <margi...@gmail.com>

 

Hi, 

 

I am trying to install PFLOTRAN using the windows subsystem for Linux instructions and am encountering issues when I make PFLOTRAN and when installing/compiling PETSc particularly with hdf5. I am using WSL/Ubuntu in a Windows 10 setting. I have a NVIDIA GPU but haven't gotten far enough to use the code to set up for it ...saw something about adding --with-cuda, so eventually would appreciate advice on how to get that working, too. I ran the regression test on the PFLOTRAN make - it failed.

 

When Installing/Compiling PETSc, it wouldn't configure hdf5 with the given options. I ended up configuring PETSc without HDF5 except for Fortran bc it wouldn't finish compiling when HDF5 is downloaded and configuration attempted. Instead, I uploaded CMAKE HDF5 separately into my directory and ran CMAKE, but am unsure if the application will be able to utilize those files as I don't know where to define the path for where they are. I also had to use a different version of BLAS to make it finish compiling).

 

I, otherwise, get the following messages/errors (snippets included below).  I need help as the instructions that I am reading online are not working for me. Is there something more current posted? I would like to use PFLOTRAN for reactive transport modeling, and so need to get those pieces working. Could you please advise on how to do setup for my situation?

 

HDF5-Related Error

hdf5 won't compile with the given options

 

PETSc

(Errors at bottom of PETSc configuration script below):

pnguyen7@DESKTOP-D85JDDR:~/petsc$ ./configure --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --download-mpich=yes --download-hdf5-fortran-bindings=yes --download-f2cblaslapack=1 --download-metis=yes --download-parmetis=yes

=============================================================================================

                         Configuring PETSc to compile on your system

=============================================================================================

=============================================================================================

  Trying to download

  https://ftp.mcs.anl.gov/pub/petsc/externalpackages/f2cblaslapack-3.8.0.q0.tar.gz for

  F2CBLASLAPACK

=============================================================================================

=============================================================================================

                    Compiling F2CBLASLAPACK; this may take several minutes

=============================================================================================

=============================================================================================

                   Installing F2CBLASLAPACK; this may take several minutes

=============================================================================================

Compilers:

  C Compiler:         arch-linux-c-opt/bin/mpicc -O3

    Version: gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0

Linkers:

  Shared linker:   arch-linux-c-opt/bin/mpicc  -shared -O3

  Dynamic linker:   arch-linux-c-opt/bin/mpicc  -shared -O3

  Libraries linked against:   -ldl

BlasLapack:

  Libraries:  -Wl,-rpath,arch-linux-c-opt/lib -Larch-linux-c-opt/lib -lf2clapack -lf2cblas

  uses 4 byte integers

MPI:

  Version:    4

  Includes:   -Iarch-linux-c-opt/include

  mpiexec: arch-linux-c-opt/bin/mpiexec

  Implementation: mpich4

  MPICH_NUMVERSION: 40002300

MPICH:

f2cblaslapack:

pthread:

cmake:

  Version:    3.22.1

  Executable: /usr/bin/cmake

metis:

  Version:    5.1.0

  Includes:   -Iarch-linux-c-opt/include

  Libraries:  -Wl,-rpath,arch-linux-c-opt/lib -Larch-linux-c-opt/lib -lmetis

python:

  Executable: /usr/bin/python3

parmetis:

  Version:    4.0.3

  Includes:   -Iarch-linux-c-opt/include

  Libraries:  -Wl,-rpath,arch-linux-c-opt/lib -Larch-linux-c-opt/lib -lparmetis

regex:

PETSc:

  Language used to compile PETSc: C

  PETSC_ARCH: arch-linux-c-opt

  PETSC_DIR: /home/pnguyen7/petsc

  Prefix: <inplace installation>

  Scalar type: real

  Precision: double

  Support for __float128

  Integer size: 4 bytes

  Single library: yes

  Shared libraries: yes

  Memory alignment from malloc(): 16 bytes

  Using GNU make: /usr/bin/gmake

xxx=========================================================================xxx

 Configure stage complete. Now build PETSc libraries with:

   make PETSC_DIR=/home/pnguyen7/petsc PETSC_ARCH=arch-linux-c-opt all

xxx=========================================================================xxx

=========================================

Now to check if the libraries are working do:

make PETSC_DIR=/home/pnguyen7/petsc PETSC_ARCH=arch-linux-c-opt check

=========================================

pnguyen7@DESKTOP-D85JDDR:~/petsc$ make PETSC_DIR=/home/pnguyen7/petsc PETSC_ARCH=arch-linux-c-opt check

Running check examples to verify correct installation

Using PETSC_DIR=/home/pnguyen7/petsc and PETSC_ARCH=arch-linux-c-opt

/usr/bin/bash: -c: line 9: unexpected EOF while looking for matching `"'

/usr/bin/bash: -c: line 15: syntax error: unexpected end of file

gmake[1]: *** [makefile:149: check] Error 2

make: *** [GNUmakefile:17: check] Error 2

 

pnguyen7@DESKTOP-D85JDDR:~/petsc$ ./configure --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --download-mpich=yes --download-hdf5=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes
=============================================================================================
                         Configuring PETSc to compile on your system
=============================================================================================
TESTING: checkCxxCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:1690)^CTraceback (most recent call last):
  File "/usr/lib/python3.10/genericpath.py", line 30, in isfile
    st = os.stat(path)
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/c/Users/user/AppData/Local/Programs/MiKTeX/miktex/bin/x64/cc++'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/pnguyen7/petsc/./configure", line 16, in <module>
    configure.petsc_configure([])
  File "/home/pnguyen7/petsc/config/configure.py", line 461, in petsc_configure
    framework.configure(out = sys.stdout)
  File "/home/pnguyen7/petsc/config/BuildSystem/config/framework.py", line 1412, in configure
    self.processChildren()
  File "/home/pnguyen7/petsc/config/BuildSystem/config/framework.py", line 1400, in processChildren
    self.serialEvaluation(self.childGraph)
  File "/home/pnguyen7/petsc/config/BuildSystem/config/framework.py", line 1375, in serialEvaluation
    child.configure()
  File "/home/pnguyen7/petsc/config/BuildSystem/config/setCompilers.py", line 2728, in configure
    self.executeTest(getattr(self,LANG.join(('check','Compiler'))))
  File "/home/pnguyen7/petsc/config/BuildSystem/config/base.py", line 138, in executeTest
    ret = test(*args,**kargs)
  File "/home/pnguyen7/petsc/config/BuildSystem/config/setCompilers.py", line 1698, in checkCxxCompiler
    if self.getExecutable(compiler, resultName = 'CXX'):
  File "/home/pnguyen7/petsc/config/BuildSystem/config/base.py", line 275, in getExecutable
    if self.checkExecutable(d, name):
  File "/home/pnguyen7/petsc/config/BuildSystem/config/base.py", line 222, in checkExecutable
    if os.path.isfile(prog) and os.access(prog, os.X_OK):
  File "/usr/lib/python3.10/genericpath.py", line 30, in isfile
    st = os.stat(path)
K

 

Errors during check:

 

pnguyen7@DESKTOP-D85JDDR:~/petsc$ make PETSC_ARCH=arch-linux-c-opt check
Running check examples to verify correct installation
Using PETSC_DIR=/home/pnguyen7/petsc and PETSC_ARCH=arch-linux-c-opt
/usr/bin/bash: -c: line 9: unexpected EOF while looking for matching `"'
/usr/bin/bash: -c: line 15: syntax error: unexpected end of file
gmake[1]: *** [makefile:149: check] Error 2
make: *** [GNUmakefile:17: check] Error 2

 

 

This works, but there's no hdf5:

 

pnguyen7@DESKTOP-D85JDDR:~/petsc$ ./configure --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --download-mpich=yes --download-hdf5-fortran-bindings=yes --download-f2cblaslapack=1 --download-metis=yes --download-parmetis=yes
=============================================================================================
                         Configuring PETSc to compile on your system
=============================================================================================
=============================================================================================
  Trying to download
  https://ftp.mcs.anl.gov/pub/petsc/externalpackages/f2cblaslapack-3.8.0.q0.tar.gz for
  F2CBLASLAPACK
=============================================================================================
=============================================================================================
                    Compiling F2CBLASLAPACK; this may take several minutes
=============================================================================================
=============================================================================================
                   Installing F2CBLASLAPACK; this may take several minutes
=============================================================================================
Compilers:
  C Compiler:         arch-linux-c-opt/bin/mpicc -O3
    Version: gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
Linkers:
  Shared linker:   arch-linux-c-opt/bin/mpicc  -shared -O3
  Dynamic linker:   arch-linux-c-opt/bin/mpicc  -shared -O3
  Libraries linked against:   -ldl
BlasLapack:
  Libraries:  -Wl,-rpath,arch-linux-c-opt/lib -Larch-linux-c-opt/lib -lf2clapack -lf2cblas
  uses 4 byte integers
MPI:
  Version:    4
  Includes:   -Iarch-linux-c-opt/include
  mpiexec: arch-linux-c-opt/bin/mpiexec
  Implementation: mpich4
  MPICH_NUMVERSION: 40002300
MPICH:
f2cblaslapack:
pthread:
cmake:
  Version:    3.22.1
  Executable: /usr/bin/cmake
metis:
  Version:    5.1.0
  Includes:   -Iarch-linux-c-opt/include
  Libraries:  -Wl,-rpath,arch-linux-c-opt/lib -Larch-linux-c-opt/lib -lmetis
python:
  Executable: /usr/bin/python3
parmetis:
  Version:    4.0.3
  Includes:   -Iarch-linux-c-opt/include
  Libraries:  -Wl,-rpath,arch-linux-c-opt/lib -Larch-linux-c-opt/lib -lparmetis
regex:
PETSc:
  Language used to compile PETSc: C
  PETSC_ARCH: arch-linux-c-opt
  PETSC_DIR: /home/pnguyen7/petsc
  Prefix: <inplace installation>
  Scalar type: real
  Precision: double
  Support for __float128
  Integer size: 4 bytes
  Single library: yes
  Shared libraries: yes
  Memory alignment from malloc(): 16 bytes
  Using GNU make: /usr/bin/gmake
xxx=========================================================================xxx
 Configure stage complete. Now build PETSc libraries with:
   make PETSC_DIR=/home/pnguyen7/petsc PETSC_ARCH=arch-linux-c-opt all
xxx=========================================================================xxx

 

 

ERRORS with make PFLOTRAN

 

o communicator_aux.o -c      -I.  `pwd`/communicator_aux.F90
/usr/bin/bash: line 1: o: command not found
make: [/home/pnguyen7/petsc/lib/petsc/conf/rules:314: communicator_aux.o] Error 127 (ignored)
o pflotran_constants.o -c      -I.  `pwd`/pflotran_constants.F90
/usr/bin/bash: line 1: o: command not found
make: [/home/pnguyen7/petsc/lib/petsc/conf/rules:314: pflotran_constants.o] Error 127 (ignored)
o string.o -c      -I.  `pwd`/string.F90
/usr/bin/bash: line 1: o: command not found
make: [/home/pnguyen7/petsc/lib/petsc/conf/rules:314: string.o] Error 127 (ignored)
o print.o -c      -I.  `pwd`/print.F90
/usr/bin/bash: line 1: o: command not found
make: [/home/pnguyen7/petsc/lib/petsc/conf/rules:314: print.o] Error 127 (ignored)
o driver.o -c      -I.  `pwd`/driver.F90
/usr/bin/bash: line 1: o: command not found
make: [/home/pnguyen7/petsc/lib/petsc/conf/rules:314: driver.o] Error 127 (ignored)
o generic.o -c      -I.  `pwd`/generic.F90
/usr/bin/bash: line 1: o: command not found
make: [/home/pnguyen7/petsc/lib/petsc/conf/rules:314: generic.o] Error 127 (ignored)
o option_checkpoint.o -c      -I.  `pwd`/option_checkpoint.F90
/usr/bin/bash: line 1: o: command not found
make: [

 

 

Regression test:

...

make: [/home/pnguyen7/petsc/lib/petsc/conf/rules:314: geomechanics_global.o] Error 127 (ignored)
o output_geomechanics.o -c      -I.  `pwd`/output_geomechanics.F90
/usr/bin/bash: line 1: o: command not found
make: [/home/pnguyen7/petsc/lib/petsc/conf/rules:314: output_geomechanics.o] Error 127 (ignored)
o geomechanics_regression.o -c      -I.  `pwd`/geomechanics_regression.F90
/usr/bin/bash: line 1: o: command not found

m

...

/usr/bin/bash: line 1: o: command not found

make: [makefile:272: pflotran] Error 127 (ignored)
gmake[1]: Entering directory '/home/pnguyen7/petsc/pflotran/src/pflotran/unittests'
./build-pfunit.sh -c  -d ../../../tpls/pfunit
ERROR: The pFUnit root directory must be provided on the command line.
gmake[1]: *** [Makefile:94: ../../../tpls/pfunit/source/libpfunit.a] Error 1
gmake[1]: Leaving directory '/home/pnguyen7/petsc/pflotran/src/pflotran/unittests'
make: *** [makefile:324: utest] Error 2

 

pnguyen7@DESKTOP-D85JDDR:~/petsc/pflotran/regression_tests$ make check
/usr/bin/python3 regression_tests.py -e ../src/pflotran/pflotran --mpiexec /home/pnguyen7/petsc/lib/petsc/bin/petsc-mpiexec.uni \
        --suite standard standard_parallel \
        --config-files ascem/1d/1d-calcite/1d-calcite.cfg

Test log file : pflotran-tests-2023-05-29_21-12-29.testlog
ERROR: executable is not a valid file: '/home/pnguyen7/petsc/pflotran/src/pflotran/pflotran'
make: [Makefile:226: check] Error 1 (ignored)

 

Here is Here is my config.log:

#endif

  Attempting to save configure hash file: arch-linux-c-opt/lib/petsc/conf/configure-hash
  Saved configure hash file: arch-linux-c-opt/lib/petsc/conf/configure-hash
Configure Actions
   These are the actions performed by configure on the filesystem
-----------------------------------------------------------------
F2CBLASLAPACK:
  Download      : Downloaded F2CBLASLAPACK into /home/pnguyen7/petsc/arch-linux-c-opt/externalpackages/f2cblaslapack-3.8.0.q0
  Install       : Installed F2CBLASLAPACK into /home/pnguyen7/petsc/arch-linux-c-opt
PETSc:
  Build         : Set default architecture to arch-linux-c-opt in lib/petsc/conf/petscvariables
  File creation : Created arch-linux-c-opt/lib/petsc/conf/reconfigure-arch-linux-c-opt.py for automatic reconfiguration
Framework:
  RDict update  : Substitutions were stored in RDict with parent None
  File creation : Created makefile configure header arch-linux-c-opt/lib/petsc/conf/petscvariables
  File creation : Created makefile configure header arch-linux-c-opt/lib/petsc/conf/petscrules
  File creation : Created configure header arch-linux-c-opt/include/petscconf.h
  File creation : Created C specific configure header arch-linux-c-opt/include/petscfix.h
  File creation : Created configure pkg header arch-linux-c-opt/include/petscpkg_version.h
Compilers:
  C Compiler:         /home/pnguyen7/petsc/arch-linux-c-opt/bin/mpicc -O3
    Version: gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
Linkers:
  Shared linker:   /home/pnguyen7/petsc/arch-linux-c-opt/bin/mpicc  -shared -O3
  Dynamic linker:   /home/pnguyen7/petsc/arch-linux-c-opt/bin/mpicc  -shared -O3
  Libraries linked against:   -ldl
BlasLapack:
  Libraries:  -Wl,-rpath,/home/pnguyen7/petsc/arch-linux-c-opt/lib -L/home/pnguyen7/petsc/arch-linux-c-opt/lib -lf2clapack -lf2cblas
  uses 4 byte integers
MPI:
  Version:    4
  Includes:   -I/home/pnguyen7/petsc/arch-linux-c-opt/include
  mpiexec: /home/pnguyen7/petsc/arch-linux-c-opt/bin/mpiexec
  Implementation: mpich4
  MPICH_NUMVERSION: 40002300
MPICH:
f2cblaslapack:
pthread:
cmake:
  Version:    3.22.1
  Executable: /usr/bin/cmake
metis:
  Version:    5.1.0
  Includes:   -I/home/pnguyen7/petsc/arch-linux-c-opt/include
  Libraries:  -Wl,-rpath,/home/pnguyen7/petsc/arch-linux-c-opt/lib -L/home/pnguyen7/petsc/arch-linux-c-opt/lib -lmetis
python:
  Executable: /usr/bin/python3
parmetis:
  Version:    4.0.3
  Includes:   -I/home/pnguyen7/petsc/arch-linux-c-opt/include
  Libraries:  -Wl,-rpath,/home/pnguyen7/petsc/arch-linux-c-opt/lib -L/home/pnguyen7/petsc/arch-linux-c-opt/lib -lparmetis
regex:
PETSc:
  Language used to compile PETSc: C
  PETSC_ARCH: arch-linux-c-opt
  PETSC_DIR: /home/pnguyen7/petsc
  Prefix: <inplace installation>
  Scalar type: real
  Precision: double
  Support for __float128
  Integer size: 4 bytes
  Single library: yes
  Shared libraries: yes
  Memory alignment from malloc(): 16 bytes
  Using GNU make: /usr/bin/gmake
xxx=========================================================================xxx
 Configure stage complete. Now build PETSc libraries with:
   make PETSC_DIR=/home/pnguyen7/petsc PETSC_ARCH=arch-linux-c-opt all
xxx=========================================================================xxx
================================================================================
Finishing configure run at Mon, 29 May 2023 20:36:17 -0700
================================================================================
"configure.log" 22289L, 1653581B                                                                  22289,1       Bot

 

I look forward to hearing from you.

 

Thank you in advance,

 

Peggy

 

--

Peggy Nguyen, M.Ed., M.S. Environmental Science, Policy and Management, Cert. Restoration Ecology

Doctoral Candidate
Environmental Science and Engineering Program

UCLA Institute of the Environment and Sustainability

Telephone: (310) 617-7436

 

 

--

Peggy Nguyen, M.Ed., M.S. Environmental Science, Policy and Management, Cert. Restoration Ecology

Doctoral Student
Environmental Science and Engineering Program

UCLA Institute of the Environment and Sustainability

Telephone: (310) 617-7436

 

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Peggy Nguyen, M.Ed., M.S. Environmental Science, Policy and Management, Cert. Restoration Ecology

Doctoral Student
Environmental Science and Engineering Program

UCLA Institute of the Environment and Sustainability

Telephone: (310) 617-7436

 

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Peggy Nguyen, M.Ed., M.S. Environmental Science, Policy and Management, Cert. Restoration Ecology

Doctoral Student
Environmental Science and Engineering Program

UCLA Institute of the Environment and Sustainability

Telephone: (310) 617-7436

[Hammond, Glenn E]

Peggy,

 

Please attach the entire file configure.log found in /home/pnguyen7/petsc.

 

Glenn

 

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