Bug 2120751 - Error compiling a PETSc program
Summary: Error compiling a PETSc program
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: petsc
Version: 36
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Antonio T. sagitter
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2022-08-23 16:37 UTC by Rafel Amer
Modified: 2022-09-12 17:38 UTC (History)
1 user (show)

Fixed In Version: petsc-3.16.4-4.fc36 petsc-3.17.4-2.fc37
Clone Of:
Environment:
Last Closed: 2022-09-04 22:45:02 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)
The file e.c (928 bytes, text/x-csrc)
2022-08-23 16:37 UTC, Rafel Amer
no flags Details

Description Rafel Amer 2022-08-23 16:37:24 UTC
Created attachment 1907168 [details]
The file e.c

Compile and run the program e.c from the book PETSc for Partial Differential Equations: Numerical Solutions in C and Python

Version-Release number of selected component: Fedora 36

How reproducible:

Steps to Reproduce:

1. Install the packages openmpi, openmpi-dev3el, petsc-openmpi and petsc-openmpi-devel
2. To have the files e.c and Makefile
3. ~$ cat Makefile
e: e.o
	${CLINKER} -o e e.o ${PETSC_LIB}

include ${PETSC_DIR}/lib64/openmpi/lib/petsc/conf/variables
include ${PETSC_DIR}/lib64/openmpi/lib/petsc/conf//rules

4. Run the commands
~$ export PETSC_DIR=/usr
~$ make e
/usr/lib64/openmpi/bin/mpicc -o e.o -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3    -I/usr/include -I/usr/include/openmpi-x86_64/petsc -I/usr/lib64/gfortran/modules/openmpi/petsc -I/usr/include/openmpi-x86_64/hypre -I/usr/include/openmpi-x86_64/superlu_dist -I/usr/include/flexiblas    `pwd`/e.c
/usr/lib64/openmpi/bin/mpicc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -fPIC -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3  -o e e.o -L/usr/lib64/openmpi/lib -L/usr//lib -L/usr/lib64/openmpi/lib -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lsuperlu_dist -lflexiblas -lptscotch -lscotch -lptscotcherr -lscotcherr -lcgns -lhdf5 -lhdf5_hl -lmetis -lm -lX11 -lquadmath -lstdc++ -ldl -lmpi -lmpi_mpifh
/usr/bin/ld: cannot open linker script file /builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [Makefile:2: e] Error 1


Actual results:

/usr/bin/ld: cannot open linker script file /builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld: No such file or directory

Expected results:

Correct compilation of the program

Additional info:

Comment 1 Fedora Update System 2022-08-24 19:13:24 UTC
FEDORA-2022-fea01db0ce has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2022-fea01db0ce

Comment 2 Fedora Update System 2022-08-24 19:13:25 UTC
FEDORA-2022-b584048fe7 has been submitted as an update to Fedora 36. https://bodhi.fedoraproject.org/updates/FEDORA-2022-b584048fe7

Comment 3 Fedora Update System 2022-08-25 08:52:35 UTC
FEDORA-2022-fea01db0ce has been pushed to the Fedora 37 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2022-fea01db0ce`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-fea01db0ce

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 4 Fedora Update System 2022-08-26 11:56:17 UTC
FEDORA-2022-b584048fe7 has been pushed to the Fedora 36 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2022-b584048fe7`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-b584048fe7

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 5 Fedora Update System 2022-09-04 22:45:02 UTC
FEDORA-2022-b584048fe7 has been pushed to the Fedora 36 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 6 Fedora Update System 2022-09-12 17:38:58 UTC
FEDORA-2022-fea01db0ce has been pushed to the Fedora 37 stable repository.
If problem still persists, please make note of it in this bug report.


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