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.
Related
I successfully use mypyc in my project and it has performed well until just a couple days ago. I now get the following error:
File "mypyc/__main__.py", line 18, in <module>
KeyError: '__file__'
Line 18 above, i.e., the line that is failing, is just
base_path = os.path.join(os.path.dirname(__file__), '..')
which I wouldn't expect to fail. I am in my venv virtualenv when I execute mypyc using the same command as has always worked before.
I thought perhaps a regression was introduced in mypyc so I used git to go back in time to see if that line had changed in any recent version of mypy, but it hadn't.
I also tried downgrading mypy to an older version that worked before but that version also failed with the same error. To be sure it wasn't being experienced by others I also checked the issues at the mypy repo on github and did a search for __file__ to see if that part of the error message showed up and it didn't. Perhaps it is some weird issue with my environment?
I experience the issue with venv virtualenvs created with Python 3.10, 3.10.1 but also 3.9.9 too. It worked fine on Python 3.10 before. Any ideas on what to investigate next?
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.
Reaching out to the wider group as I am totally stumped trying to install Intel MPSS 4.x for my Xeon Phi 7220P.
I followed the precise steps in this link: Intel MPSS Linux User Guide Rev 4.4.1, and did it 3 times to make sure I wasn't missing any steps or making mistakes, but keep getting the following error readout:
modprobe: WARNING: Module mic_x200_dma not found.
modprobe: WARNING: Module scif_bus not found.
modprobe: WARNING: Module vop_bus not found.
modprobe: WARNING: Module cosm_bus not found.
modprobe: WARNING: Module scif not found.
modprobe: WARNING: Module vop not found.
modprobe: WARNING: Module mic_cosm not found.
modprobe: WARNING: Module mic_x200 not found.
As a result of this, I cant do the basic MPSS commands such as micctrl -s etc nor use the Xeon Phi whatsoever.
I am running Centos 7 (862 kernel), and know its not listed in the Intel pdf, but did not think this should be causing an issue as it seems that the above kernel modules are simply not being installed seemingly from Intel MPSS - but not sure if this diagnosis is correct.
Would appreciate your help - many thanks in advance!
It is complaining about that because at one point your kernel got updated from 3.10.0-514.el7 to a later version, (it happens automatically when you do a yum update, annoying I know)
Check your kernel version by running
uname -r
When you installed/compiled all the modules they were placed into /lib/modules/3.10.0-514.el7.x86_64 which is where the source code you have exported to.
You have 2 options:
Recompile the source code to work for your current kernel version (which is a pain and has it's own problems)
Revert your host kernel back to 3.10.0-514.el7 via grub config (example here) and everything will work nicely
I too struggled with this very much in the beginning and I had to read pretty much every line of source code and spend countless hours debugging until I found out. At this point there is nothing I do not know about the Xeon Phi x100/x200.
The documentation is not bad, but it didn't cover this bare essential, which is frustrating.
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.
I ran into an odd issue that I cannot fix in any way and I was hoping someone here may have a better understanding of whats wrong;
I am unable to use RWebLogo package - even run the simplest examples due to the same missing Ghostscript error.
e.g. running:
library(RWebLogo)
aln <- c('CCAACCCAA', 'CCAACCCTA', 'AAAGCCTGA', 'TGAACCGGA')
weblogo(seqs=aln, file.out='mylogo.pdf')
Throws this error:
Traceback (most recent call last):
File "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogo", line 71, in <module>
weblogolib._cli.main()
File "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogolib/_cli.py", line 82, in main
formatter(data, format, opts.fout)
File "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogolib/__init__.py", line 757, in pdf_formatter
gs = GhostscriptAPI()
File "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogolib/__init__.py", line 196, in __init__
raise EnvironmentError("Could not find Ghostscript on path."
EnvironmentError: Could not find Ghostscript on path. There should be either a gs executable or a gswin32c.exe on your system's path
I have installed ghostscript ver 9.15 with configure/make/install in the terminal and then added the PATH to bash profile and executed it. When I run gs in the terminal it works, confirming it is set to the system path, yet the same error still occurs. Even after rebooting.
I tried adding the gs to the environment in R directly:
Sys.setenv(R_GSCMD = "/Applications/ghostscript-9.15/bin/gs")
which also hasn't helped... Gives exactly the same error. When I search the R environment it shows that gs is there.
Important version information:
MAC: OS Yosemite 10.10.1;
R version 3.1.1 (2014-07-10);
Platform: x86_64-apple-darwin10.8.0 (64-bit);
RWebLogo_1.0.3
Do you know of any issue that may have cause this problem? I'm new to programming, so I am worried I may be missing something basic. I would be grateful for any advice. Thank you!
I have gotten in touch with Omar, the author of RWebLogo, and he has been really helpful in pinpointing my problems and resolving the issue.
First, he advised to run the RWebLogo on a test sequence on the terminal:
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogo -f test_seqs.txt -o ~/Desktop/out.pdf -F pdf
Change the base directory (everything before extdata/weblogo …) of the script above to be whatever the command below gives you in R:
system.file(package = 'RWebLogo')
I ran it and got a new error: the lack of numpy. I actually had the numpy installed but without full user privileges. After reinstalling numpy, the RWebLogo was successfully running from the terminal.
Still, the RStudio was throwing a GhostScript error. Omar suggested that there is a problem with an older version of RStudio running on Yosemite (I currently have 10.10.1), and sent me a link to an updated RStudio version where the problem was fixed.
http://www.r-bloggers.com/r-and-rstudio-incompatibility-with-yosemite-mac-os-x-10-10/
I got the updated RStudio and everything works great there right now. Hope this helps someone with a similar issue!