I am installing mpi4py using pip using the command pip3 install mpi4py, on a centos7 system.
I get this error:
/glade/u/apps/ch/opt/openmpi/4.0.5/intel/19.0.5/bin/mpicc _configtest.o -L/glade/u/apps/ch/opt/python/3.7.9/gnu/9.1.0/lib -Lbuild/temp.linux-x86_64-3.7 -Wl,--enable-new-dtags,-R/glade/u/apps/ch/opt/python/3.7.9/gnu/9.1.0/lib -o _configtest
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: /opt/pbs/lib/libpbs.so.0: undefined reference to `sec_set_context'
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!
----------------------------------------
Does anybody have any tips?
In this case on Cheyenne's HPC cluster, you will likely need to add these arguments to your compilation/link commands -L/opt/pbs/lib -Wl,-rpath,/opt/pbs/lib -lsec or reload the ncarcompilers module.
Nevertheless, I recommend you reach out to CISL's helpdesk at NCAR for any similar problems you encounter on our system as there are dedicated teams of people to help users resolve issues like this.
Related
I need execute Data Fusion pipelines from Composer, using de operatos for this:
from airflow.providers.google.cloud.operators.datafusion import (
CloudDataFusionCreateInstanceOperator,
CloudDataFusionCreatePipelineOperator,
CloudDataFusionDeleteInstanceOperator,
CloudDataFusionDeletePipelineOperator,
CloudDataFusionGetInstanceOperator,
CloudDataFusionListPipelinesOperator,
CloudDataFusionRestartInstanceOperator,
CloudDataFusionStartPipelineOperator,
CloudDataFusionStopPipelineOperator,
CloudDataFusionUpdateInstanceOperator,
)
The issue I have is about modulo "apache-airflow-backport-providers-google", with the support of this links i knew what I need to use this modulo:
reference to install the modulo in airflow instance (answered by #Gonzalo Pérez Fernández): https://airflow.apache.org/docs/apache-airflow-providers-google/stable/operators/cloud/datafusion.html
when i tried to install python dependency on Composer like PyPi Package i get this error:
UPDATE operation on this environment failed 7 minutes ago with the following error message:
Failed to install PyPI packages.
apache-airflow-providers-google 5.0.0 has requirement google-ads>=12.0.0, but you have google-ads 7.0.0. Check the Cloud Build log at https://console.cloud.google.com/cloud-build/builds/a2ecf37a-4c47-4770-9489-6fb65e87d82f?project=341768372632 for details. For detailed instructions see https://cloud.google.com/composer/docs/troubleshooting-package-installation
the log deail is:
apache-airflow-providers-google 5.0.0 has requirement google-ads>=12.0.0, but you have google-ads 7.0.0.
apache-airflow-backport-providers-google 2021.3.3 has requirement apache-airflow~=1.10, but you have apache-airflow 2.1.2+composer.
The command '/bin/sh -c bash installer.sh $COMPOSER_PYTHON_VERSION fail' returned a non-zero code: 1
ERROR
ERROR: build step 0 "gcr.io/cloud-builders/docker" failed: step exited with non-zero status: 1
is there any way to use de module "apache-airflow-backport-providers-google" without depedency issues on composer instance?, or What would be the best way to use data fusion operators no need to change or parse package versions in python?.
Composer Image version used:
composer-1.17.0-airflow-2.1.2
Thanks.
There is no need to install apache-airflow-backport-providers-google in Airflow 2.0+. This package actually backports Airflow 2 operators into Airflow 1.10.*. In addition, in Composer version composer-1.17.0-airflow-2.1.2 the apache-airflow-providers-google==5.0.0 package is already installed according to the documentation. You should be able to import the Data Fusion operators with the code snippet you posted as is.
However, if this is not the case, you should probably handle the conflict shown in the logs when trying to reinstall apache-airflow-providers-google==5.0.0:
apache-airflow-providers-google 5.0.0 has requirement google-ads>=12.0.0, but you have google-ads 7.0.0.
You can add the requirement for google-ads=12.0.0 in your PyPi dependencies and see if it works.
I have tried running the Openmdao paraboloid tutorial as well as benchmarks and I consistently receive the same error which reads as following:
[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 http://www.mcs.anl.gov/petsc/documentation/faq.html#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: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash
---------------------------------------------------------------------
MPI_abort was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 59.
NOTE: invoking MPI_ABORT causes MPI to kill all MPI processes.
you may or may not see output from other processes, depending on exactly when Open MPI kills them.
I don't understand why this error is occurring and what I can do to be able to run OpenMDAO without getting this error. Can you please help me with this?
Something has not gone well with your PETSc install. Its hard to debug that from afar though. It could be in your MPI install, or your PETSc install, or your petsc4py install. I suggest not install PETSc or PETSc4Py through pip though. I've had mixed success with that. Both can be installed from source without tremendous difficulty.
However, to run the tutorials you don't need to have PETSc installed. You could remove those packages and the tutorials will run correctly in serial for you
I'm trying to install cunn for Torch but make install fails. Cuda is 7.5.27 because 8 doesn't support OSX 10.10 anymore.
I've been trying to debug this for a while, but I'm running out of things to try.
While searching solution I saw few others having a similar problem (https://github.com/TRIQS/cthyb/issues/8, https://github.com/jcjohnson/neural-style/issues/134) but didn't find any solution that would fix this. It seems that this is a general problem related to OSX/Xcode and not necessarily cunn.
All help is much appreciated.
$ luarocks install cunn
...
...
-- Installing: /Users/foo/torch/install/lib/luarocks/rocks/cunn/scm-1/lib/libTHCUNN.so
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: for:
/Users/foo/torch/install/lib/luarocks/rocks/cunn/scm-1/lib/libTHCUNN.so (for architecture x86_64) option "-add_rpath /usr/local/cuda/lib"
would duplicate path, file already has LC_RPATH for: /usr/local/cuda/lib
The issue went away when I did ./clean.sh in ~/torch followed by ./update.sh. I still don't have any idea what was the problem.
Today's (1 Mar 2016) OpenSSL release has caused the following error when running Plone/Zope
.buildout/eggs/ZODB3-3.10.5-py2.7-linux-x86_64.egg/persistent/cPersistence.so: undefined symbol: SSLv2_method
It's hard to see what's going on since it's a binary file. I also tried updating to ZODB3 3.11.0 which yields the following traceback
.buildout/eggs/ZConfig-2.9.0-py2.7.egg/ZConfig/loader.py", line 217, in schemaComponentSource
package=package)
ZConfig.SchemaResourceError: could not load package ZServer:
.buildout/eggs/zope.security-3.7.4-py2.7-linux-x86_64.egg/zope/security/_proxy.so: undefined symbol: SSLv2_method
Package name: 'ZServer'
File name: 'component.xml'
Package path: None
Is there any workaround for this other than reverting OpenSSL?
zope security is a compiled egg, like all the ones ending with -py2.7-linux-x86_64.egg.
As the traceback says, it cannot find anymore a symbol.
Probably you have to recompile it with the new openssl-dev.
I would try (on a development server first):
backup your compiled egg (mkdir eggs-backup && mv `eggs/zope.security-3.7.4-py2.7-linux-x86_64.egg eggs-backup/)
rerun buildout
This will recompile your missing egg.
Hopefully it works and hopefully it is the only one linked to that library.
Anyway, dependending on the way you patched openssl you may have a lot of other issues (I am thinking about Python, urllib*, curl, wget, ...)
OpenSSL 1.0.2g by default doesn't build with SSLv2 (because of the recent DROWN attack). You may need to manually build it without OPENSSL_NO_SSL2 flag.
(but in fact you shouldn't do this if you're doing some server-related stuff, there is a serious security reason because of which it was disabled, see https://drownattack.com)
I was able to resolve this by upgrading python to 2.7.10+, and then upgrading Pillow and lxml.
After going through a lot of sites about best terminal for system admins I was trying to install on Cygwin. Unfortunately, I did not find any good site with instruction about how to do it.
Is anyone done this before? Please help me with steps and packages that I need to install.
Also is there any terminals I can try (like Cygwin)?
I don't know since what version, but now you can install terminator just from the Cygwin installer. And runs great
Regards
If you don't want to use cygwinports, you can actually install all of terminator's dependencies from the cygwin installer, except for terminator itself.
In the cygwin installer select and install:
python-dbus
python-gobject
python-gtk2.0
python-vte (under GNOME tab for some reason)
GConf2
Then, pull down the latest terminator tarball from https://launchpad.net/terminator/+download and extract it somewhere. In a administrator terminal just run python setup.py install and as long as you have a running X server just running terminator will work perfectly.
The sources about how to install terminator are a bit obscures. What I did, and may help you, was this: (although I'm still having segmentation faults errors)
Update your Cygwin to the latest
Open a Cygwin terminal and run: (if you have the x86 version use that. The idea of this step is to use Cygwin Ports)
cygstart -- /your/cygwin/path/setup-x86_64.exe -K http://cygwinports.org/ports.gpg
In the section Choose A Download Site:
Add "http://downloads.sourceforge.net/cygwin-ports"
Add " ftp://ftp.cygwinports.org/pub/cygwinports"
Select another mirror close to you
Check that you have a total of three URLs selected
It may show you warning about not loading the .ini configuration but ignore them (Note: I looked for different port URLs but the official ones threw me errors and I could not pass this step, that's why I used alternatives URLs)
First, you need to install the packages for the X Window:
http://x.cygwin.com/docs/ug/setup.html
Basically they are:
xorg-server (required, the Cygwin/X X Server)
xinit (required, scripts for starting the X server: xinit, startx, startwin (and a shortcut on the Start Menu to run it), startxdmcp.bat )
xorg-docs (optional, man pages)
Also search and select the terminator package
It takes quite a while before it finishes.
Go to Start->All Programs->Cygwin-X->X Win Server (windows tool bar)
A xterm window should open. Type:
terminator
You should know have terminator with Cygwin.
Note: After I run terminator I get this error:
/usr/lib/python2.7/site-packages/terminatorlib/terminator.py:87: Warning: Attempt to add property GnomeProgram::sm-connect after class was initialised
self.gnome_program = gnome.init(APP_NAME, APP_VERSION)
/usr/lib/python2.7/site-packages/terminatorlib/terminator.py:87: Warning: Attempt to add property GnomeProgram::show-crash-dialog after class was initialised
self.gnome_program = gnome.init(APP_NAME, APP_VERSION)
/usr/lib/python2.7/site-packages/terminatorlib/terminator.py:87: Warning: Attempt to add property GnomeProgram::display after class was initialised
self.gnome_program = gnome.init(APP_NAME, APP_VERSION)
/usr/lib/python2.7/site-packages/terminatorlib/terminator.py:87: Warning: Attempt to add property GnomeProgram::default-icon after class was initialised
self.gnome_program = gnome.init(APP_NAME, APP_VERSION)
Warning: python-keybinder is not installed. This means the hide_window shortcut will be unavailable
Unable to bind hide_window key, another instance/window has it.
Segmentation fault (core dumped)
I've looking to fix this issue but sadly I couldn't find anything. If you use Cygwin x86 your outcome can be different.
Hope this can help you.