I am trying to run a program using mpirun command (as shown below).
mpirun -np 4 python test.py
But I am getting following warning first:
hwloc/linux: Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
hwloc/linux: Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
hwloc/linux: Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
hwloc/linux: Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
Program also depends on PETSc, after the above warning, it shows following error:
[1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[1]PETSC ERROR: likely location of problem given in stack below
[1]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[1]PETSC ERROR: INSTEAD the line number of the start of the function
[1]PETSC ERROR: is given.
[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[1]PETSC ERROR: Signal received
[1]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.15.5, Sep 29, 2021
[1]PETSC ERROR: Unknown Name on a real-debug named skynet by pavan Sat Jun 18 10:30:04 2022
[1]PETSC ERROR: Configure options --PETSC_ARCH=real-debug --with-scalar-type=real --with-debugging=1 --with-mpi-dir=/home/pavan/packages/openmpi-4.0.7/opt-gfortran --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
[1]PETSC ERROR: #1 User provided function() at unknown file:0
[1]PETSC ERROR: Checking the memory for corruption.
[2]PETSC ERROR: ------------------------------------------------------------------------
[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[2]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[2]PETSC ERROR: likely location of problem given in stack below
[2]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[2]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[2]PETSC ERROR: INSTEAD the line number of the start of the function
[2]PETSC ERROR: is given.
[2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[2]PETSC ERROR: Signal received
[2]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[2]PETSC ERROR: Petsc Release Version 3.15.5, Sep 29, 2021
[2]PETSC ERROR: Unknown Name on a real-debug named skynet by pavan Sat Jun 18 10:30:04 2022
[2]PETSC ERROR: Configure options --PETSC_ARCH=real-debug --with-scalar-type=real --with-debugging=1 --with-mpi-dir=/home/pavan/packages/openmpi-4.0.7/opt-gfortran --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
[2]PETSC ERROR: #1 User provided function() at unknown file:0
[2]PETSC ERROR: Checking the memory for corruption.
[3]PETSC ERROR: ------------------------------------------------------------------------
[3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[3]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[3]PETSC ERROR: likely location of problem given in stack below
[3]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[3]PETSC ERROR: INSTEAD the line number of the start of the function
[3]PETSC ERROR: is given.
[3]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[3]PETSC ERROR: Signal received
[3]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[3]PETSC ERROR: Petsc Release Version 3.15.5, Sep 29, 2021
[3]PETSC ERROR: Unknown Name on a real-debug named skynet by pavan Sat Jun 18 10:30:04 2022
[3]PETSC ERROR: Configure options --PETSC_ARCH=real-debug --with-scalar-type=real --with-debugging=1 --with-mpi-dir=/home/pavan/packages/openmpi-4.0.7/opt-gfortran --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
[3]PETSC ERROR: #1 User provided function() at unknown file:0
[3]PETSC ERROR: Checking the memory for corruption.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: INSTEAD the line number of the start of the function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.15.5, Sep 29, 2021
[0]PETSC ERROR: Unknown Name on a real-debug named skynet by pavan Sat Jun 18 10:30:04 2022
[0]PETSC ERROR: Configure options --PETSC_ARCH=real-debug --with-scalar-type=real --with-debugging=1 --with-mpi-dir=/home/pavan/packages/openmpi-4.0.7/opt-gfortran --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
[0]PETSC ERROR: #1 User provided function() at unknown file:0
[0]PETSC ERROR: Checking the memory for corruption.
I am new to mpi, so I don't really know what is going here. Any help will be much appreciated. Following are the additional details which might be useful:
System: Ubuntu 22.04
OpenMPI - 4.0.7
PETSc - 3.15.5. Configured PETSc as follows:
./configure --PETSC_ARCH=$PETSC_ARCH --with-scalar-type=real --with-debugging=1 --with-mpi-dir=$MPI_INSTALL_DIR \
--download-metis=yes --download-parmetis=yes --download-superlu_dist=yes \
--with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
Python - 3.9.12
gfortran - 9.4.0
gcc - 9.4.0
Related
AS arch/arm64/mm/proc.o
../arch/arm64/mm/proc.S: Assembler messages:
../arch/arm64/mm/proc.S:283: Error: unknown mnemonic `pte_to_phys' -- `pte_to_phys cur_pmdp,pud'
../arch/arm64/mm/proc.S:302: Error: unknown mnemonic `pte_to_phys' -- `pte_to_phys cur_ptep,pmd'
Fixing an issue error build
I am using MacOSbigsur, Macbook Pro, M1 Chip,
I installed Virtual box the latest version 6.1.26r145957, use this command for confirmation (VBoxManage --version).
I installed Vagrant 2.2.18, use this command for confirmation (Vagrant --version).
I clone the repo from https://box.scotch.io/, and then type on terminal "vagrant up"
Following an error occurs, I try many solutions available on the internet but not fixed. I uninstall both software and re-install did not work for me, permission is ok from system preference.
There was an error while executing VBoxManage, a CLI used by Vagrant
for controlling VirtualBox. The command and stderr is shown below.
Command: ["hostonlyif", "create"]
Stderr: 0%...
Progress state: NS_ERROR_FAILURE
VBoxManage: error: Failed to create the host-only adapter
VBoxManage: error: VBoxNetAdpCtl: Error while adding new interface: failed to open
/dev/vboxnetctl: No such file or directory
VBoxManage: error: Details: code NS_ERROR_FAILURE (0x80004005), component
HostNetworkInterfaceWrap, interface IHostNetworkInterface
VBoxManage: error: Context: "RTEXITCODE handleCreate(HandlerArg *)" at line 95 of file VBoxManageHostonly.cpp
Possible Solution: sudo "/Library/Application Support/VirtualBox/LaunchDaemons/VirtualBoxStartup.sh" restart
when I run this command its shows the following errors
Loading VBoxDrv.kext
Incompatible architecture: Binary is for x86_64, but needed arch arm64e
Error: Failed to load org.virtualbox.kext.VBoxDrv
Loading VBoxUSB.kext
Incompatible architecture: Binary is for x86_64, but needed arch arm64e
Error: Failed to load org.virtualbox.kext.VBoxUSB
Loading VBoxNetFlt.kext
Incompatible architecture: Binary is for x86_64, but needed arch arm64e
Error: Failed to load org.virtualbox.kext.VBoxNetFlt
Loading VBoxNetAdp.kext
Incompatible architecture: Binary is for x86_64, but needed arch arm64e
Error: Failed to load org.virtualbox.kext.VBoxNetAdp
Executing: /usr/bin/kmutil unload -b org.virtualbox.kext.VBoxNetAdp
Error occurred unloading extensions: Missing extension with identifier org.virtualbox.kext.VBoxNetAdp : Incompatible
architecture: Binary is for x86_64, but needed arch arm64e
Executing: /usr/bin/kmutil unload -b org.virtualbox.kext.VBoxNetFlt
Error occurred unloading extensions: Missing extension with identifier org.virtualbox.kext.VBoxNetFlt : Incompatible
architecture: Binary is for x86_64, but needed arch arm64e
Executing: /usr/bin/kmutil unload -b org.virtualbox.kext.VBoxUSB
Error occurred unloading extensions: Missing extension with identifier org.virtualbox.kext.VBoxUSB : Incompatible architecture: Binary is for x86_64, but needed arch arm64e
Executing: /usr/bin/kmutil unload -b org.virtualbox.kext.VBoxDrv
Error occurred unloading extensions: Missing extension with identifier org.virtualbox.kext.VBoxDrv : Incompatible architecture: Binary is for x86_64, but needed arch arm64e
Fatal error: VirtualBox
I had a similar error.
Stderr: 0%...
Progress state: NS_ERROR_FAILURE
VBoxManage: error: Failed to create the host-only adapter
VBoxManage: error: VBoxNetAdpCtl: Error while adding new interface: failed to open /dev/vboxnetctl: No such file or directory
VBoxManage: error: Details: code NS_ERROR_FAILURE (0x80004005), component HostNetworkInterfaceWrap, interface IHostNetworkInterface
VBoxManage: error: Context: "RTEXITCODE handleCreate(HandlerArg *)" at line 95 of file VBoxManageHostonly.cpp
Was able resolve simply by going to security settings and adding allow from Oracle.
For me this occurred after updating Mac OS, Oracle VB and Vagrant. Currently on Mac Os Monterey 12.3.1
It is a test-drive example "https://flutter.io/get-started/test-drive/#terminal"
I have got the following error, please comment how to resolve this issue.
Xcode's output:
↳
=== BUILD TARGET Runner OF PROJECT Runner WITH CONFIGURATION Debug ===
clang-3.5: error: unknown argument: '-gmodules'
clang-3.5: error: unknown argument: '-fbuild-session-file=/Users/nelson/Library/Developer/Xcode/DerivedData/ModuleCache.noindex/Session.modulevalidation'
clang-3.5: error: no such file or directory: '/Users/nelson/Library/Developer/Xcode/DerivedData/Runner-ctvpprsqskddfxbtqtsepwpaebqm/Index/DataStore'
clang-3.5: error: option '-fmodules-validate-once-per-build-session' requires '-fbuild-session-timestamp=<seconds since Epoch>'
Command /usr/local/bin/clang-omp failed with exit code 1
clang-3.5: error: unknown argument: '-gmodules'
clang-3.5: error: unknown argument: '-fbuild-session-file=/Users/nelson/Library/Developer/Xcode/DerivedData/ModuleCache.noindex/Session.modulevalidation'
clang-3.5: error: no such file or directory: '/Users/nelson/Library/Developer/Xcode/DerivedData/Runner-ctvpprsqskddfxbtqtsepwpaebqm/Index/DataStore'
clang-3.5: error: option '-fmodules-validate-once-per-build-session' requires '-fbuild-session-timestamp=<seconds since Epoch>'
Command /usr/local/bin/clang-omp failed with exit code 1
=== BUILD TARGET Runner OF PROJECT Runner WITH CONFIGURATION Debug ===
error: the following command failed with exit code 1 but produced no further output
CompileC /Users/nelson/Library/Developer/Xcode/DerivedData/Runner-ctvpprsqskddfxbtqtsepwpaebqm/Build/Intermediates.noindex/Runner.build/Debug-iphonesimulator/Runner.build/Objects-normal/x86_64/Runner_vers.o /Users/nelson/Library/Developer/Xcode/DerivedData/Runner-ctvpprsqskddfxbtqtsepwpaebqm/Build/Intermediates.noindex/Runner.build/Debug-iphonesimulator/Runner.build/DerivedSources/Runner_vers.c normal x86_64 c com.apple.compilers.llvm.clang.1_0.compiler
clang-3.5: error: unknown argument: '-gmodules'
clang-3.5: error: unknown argument: '-fbuild-session-file=/Users/nelson/Library/Developer/Xcode/DerivedData/ModuleCache.noindex/Session.modulevalidation'
clang-3.5: error: no such file or directory: '/Users/nelson/Library/Developer/Xcode/DerivedData/Runner-ctvpprsqskddfxbtqtsepwpaebqm/Index/DataStore'
clang-3.5: error: option '-fmodules-validate-once-per-build-session' requires '-fbuild-session-timestamp=<seconds since Epoch>'
Command /usr/local/bin/clang-omp failed with exit code 1
clang-3.5: error: unknown argument: '-gmodules'
clang-3.5: error: unknown argument: '-fbuild-session-file=/Users/nelson/Library/Developer/Xcode/DerivedData/ModuleCache.noindex/Session.modulevalidation'
clang-3.5: error: no such file or directory: '/Users/nelson/Library/Developer/Xcode/DerivedData/Runner-ctvpprsqskddfxbtqtsepwpaebqm/Index/DataStore'
clang-3.5: error: option '-fmodules-validate-once-per-build-session' requires '-fbuild-session-timestamp=<seconds since Epoch>'
Command /usr/local/bin/clang-omp failed with exit code 1
Could not build the application for the simulator.
Error launching application on iPhone 7 Plus.
I have resolved the issue as the following:
If you look at the question carefully, it triggered an outdated version of clang 3.5, I uninstalled an outdated version and installed a new one.
remove clang-omp from os x
$ brew uninstall clang-omp
After uninstall clang-omp, flutter installer required to update to the latest version. Actually, I did the update before but I did it again.
$ flutter upgrade
I try to run flutter again but it cannot be compiled. It was missing clang-omp
$ flutter run
=== BUILD TARGET Runner OF PROJECT Runner WITH CONFIGURATION Debug ===
error: can't exec '/usr/local/bin/clang-omp' (No such file or directory)
Command /usr/local/bin/clang-omp failed with exit code 71
error: can't exec '/usr/local/bin/clang-omp' (No such file or directory)
Command /usr/local/bin/clang-omp failed with exit code 71
Because it required an updated version of clang during compilation. I installed llvm
$ brew install llvm
and update the PATH accordingly.
echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> ~/.bash_profile
Compile the application again, it was compiled successfully.
$ flutter run
Launching lib/main.dart on iPhone 7 Plus in debug mode...
Starting Xcode build...
├─Assembling Flutter resources... 1.1s
└─Compiling, linking and signing... 8.6s
Xcode build done. 11.3s
Syncing files to device iPhone 7 Plus... 3.9s
🔥 To hot reload changes while running, press "r". To hot restart (and rebuild state), press "R".
An Observatory debugger and profiler on iPhone 7 Plus is available at: http://127.0.0.1:8100/
For a more detailed help message, press "h". To quit, press "q".
Initializing hot reload...
Reloaded 0 of 391 libraries in 486ms.
I am posting a question because of the problem:
cc: error: unknown argument: '-fformat-extensions'
The following error occurred while compiling FreeBSD src with gcc.
Below is a log.
--------------------------------------------------------------
>>> stage 3.1: making dependencies
--------------------------------------------------------------
cc: error: unknown argument: '-fformat-extensions'
--- vmx_genassym.o ---
*** [vmx_genassym.o] Error code 1
make[4]: stopped in /usr/KRSense/tmp/FreeBSD-src/sys/modules/vmm
1 error
make[4]: stopped in /usr/KRSense/tmp/FreeBSD-src/sys/modules/vmm
--- depend_subdir_vmm ---
*** [depend_subdir_vmm] Error code 2
The FreeBSD system compiler has customer patches which adds the (curiously named) -fformat-extensions option:
Why can't lang/gcc4X compilers build kernel modules?
You will have to use the system compiler or another compiler which has been patched in the same way.
I try to compile my Gradle/Kotline Project on my new Mac and getting the same error 'Resource not found'-like errors for all my gradle projects. Any ideas whats wrong? The same project for example works on the latest Docker 'primetoninc/jdk'.
mac:nextlevel2017-kotline robert.rajakone$ ./gradlew build
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.gradle.internal.reflect.JavaMethod (file:/Users/robert.rajakone/.gradle/wrapper/dists/gradle-3.5.1-all/42vjebfdws9pjts3l4bouoq0p/gradle-3.5.1/lib/gradle-base-services-3.5.1.jar) to method java.lang.ClassLoader.getPackages()
WARNING: Please consider reporting this to the maintainers of org.gradle.internal.reflect.JavaMethod
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
:compileKotlin FAILED
FAILURE: Build failed with an exception.
* What went wrong:
Could not resolve all dependencies for configuration ':compileClasspath'.
> Could not find org.springframework.boot:spring-boot-starter-web:.
Searched in the following locations:
https://repo1.maven.org/maven2/org/springframework/boot/spring-boot-starter-web//spring-boot-starter-web-.pom
https://repo1.maven.org/maven2/org/springframework/boot/spring-boot-starter-web//spring-boot-starter-web-.jar
https://repo.spring.io/snapshot/org/springframework/boot/spring-boot-starter-web//spring-boot-starter-web-.pom
https://repo.spring.io/snapshot/org/springframework/boot/spring-boot-starter-web//spring-boot-starter-web-.jar
https://repo.spring.io/milestone/org/springframework/boot/spring-boot-starter-web//spring-boot-starter-web-.pom
https://repo.spring.io/milestone/org/springframework/boot/spring-boot-starter-web//spring-boot-starter-web-.jar
Required by:
project :
> Could not find org.springframework.boot:spring-boot-starter-data-jpa:.
Required by:
project :
* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
BUILD FAILED
Total time: 4.354 secs
mac:nextlevel2017-kotline robert.rajakone$ uname -a
Darwin mac 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
mac:nextlevel2017-kotline robert.rajakone$ ./gradlew -version
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass (file:/Users/robert.rajakone/.gradle/wrapper/dists/gradle-3.5.1-all/42vjebfdws9pjts3l4bouoq0p/gradle-3.5.1/lib/groovy-all-2.4.10.jar) to method java.lang.Object.finalize()
WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.reflection.CachedClass
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
------------------------------------------------------------
Gradle 3.5.1
------------------------------------------------------------
Build time: 2017-06-16 14:36:27 UTC
Revision: d4c3bb4eac74bd0a3c70a0d213709e484193e251
Groovy: 2.4.10
Ant: Apache Ant(TM) version 1.9.6 compiled on June 29 2015
JVM: 9 (Oracle Corporation 9+181)
OS: Mac OS X 10.12.6 x86_64
mac:nextlevel2017-kotline robert.rajakone$