I just installed Snakemake (with sudo) on a shared system, and when I run it, even snakemake --version, I get the strange error:
murray#alina:~$ snakemake --version
/usr/local/lib/python3.7/site-packages/pulp/apis/gurobi_api.py:297: UserWarning: GUROBI error:
ERROR 10009: No Gurobi license found (user murray, host alina, hostid da781c18, cores 64)
.
warnings.warn('GUROBI error: {}.'.format(out))
5.31.1
I understand that this error is related to licensing issues with the Gurobi solver (or at least its API), that is installed on the system, however, why should running Snakemake elicit this error? Fixing this, or even just squelching the error (and the resulting gurobi.log file which gets created in the directory where the snakemake --version command is run) would be much appreciated.
Related
When trying to cmake a CGAL example, I get
CMake Error: Remove failed on file:
/cgal/example/CMakeFiles/CMakeTmp/cmTC_9e180.exe: System Error: Device or resource busy
Working under Win10 + Msys2.
CGAL was obtained via pacman (local/mingw-w64-x86_64-cgal 4.13-1).
Since I did not find the CGAL examples in any Msys2 package,
it was copied from file /usr/share/doc/libcgal13/examples.tar.gz, which was obtained in an Ubuntu system with
$ sudo apt-get install libcgal-demo
The example is reconstruction_surface_mesh.cpp from examples/Advancing_front_surface_reconstruction.
I wouldn't know if the origin of the error is specific to my CMakeLists.txt, or else.
Related, but AFAICT not providing the answer:
https://cmake.org/pipermail/cmake-developers/2010-November/012619.html
https://gitlab.kitware.com/cmake/cmake/issues/17566
https://github.com/TadasBaltrusaitis/OpenFace/issues/634
CMake: how to use INTERFACE_INCLUDE_DIRECTORIES with ExternalProject?
https://www.google.com/search?safe=off&q=CMake+Error+in+CMakeLists.txt%3A+++Imported+target+includes+non-existent+path+in+its+INTERFACE_INCLUDE_DIRECTORIES.++Possible+reasons+include
I was trying to install NTL library on ubuntu, and after using "make", I get this error :
GMP version check (6.0.0/6.1.0)
*** version number mismatch: inconsistency between gmp.h and libgmp
Aborted (core dumped)
makefile:346: recipe for target 'setup3' failed
make[1]: *** [setup3] Error 134
make[1]: Leaving directory '/mnt/c/Users/pc-admin/ntl-11.0.0/ntl-11.0.0/src'
makefile:310: recipe for target 'setup-phase' failed
make: *** [setup-phase] Error 2
I saw the posts
https://gmplib.org/list-archives/gmp-discuss/2009-March/003663.html
http://www.mpfr.org/faq.html#undef_ref1
But still that didnt quite help.
Currently my usr/local/lib has
XXX#SECURE2:/usr/local/lib$ ls
libgmp.a libgmp.so libgmp.so.23.0.3 libmpfr.la libmpfr.so.6 libmpir.a libmpir.so libmpir.so.23.0.3 python3.5
libgmp.la libgmp.so.23 libmpfr.a libmpfr.so libmpfr.so.6.0.1 libmpir.la libmpir.so.23 pkgconfig
and /usr/local/include has
XXX#SECURE2:/usr/local/include$ ls
gmp.h mpf2mpfr.h mpfr.h mpir.h
Tried changing environment paths as
C_INCLUDE_PATH=usr/local/include
LIBRARY_PATH=usr/local/lib
LD_LIBRARY_PATH=usr/local/lib
Somehow I don't understand how to solve. Any help would be highly appreciated! Thanks for your patience
I encountered this problem today when I installed GMP after NTL Makefile lets me do so.
The following command seems to help:
sudo ldconfig
I met the same problem.It was because of the library's version.
First I installed gmp-6.1.2(using configure,make,make install command),and then I downloaded ntl-11.3.2,input configure and make commands.And the problem appeared:
GMP version check (6.1.2/6.1.0)
*** version number mismatch: inconsistency between gmp.h and libgmp
Aborted (core dumped)
makefile:353: recipe for target 'setup3' failed
I guessed maybe I need to install gmp 6.1.0.So I first entered gmp-6.1.2 directory,using command sudo make uninstall,then downloaded gmp-6.1.0 and the problem was solved.
Maybe you can have a try uninstalling gmp 6.0.0,installing 6.1.0.
I figured out a solution, start again and let the Wizard figure it out.
First, get rid of everything we did before
make clobber
./configure
Then edit the makefile and enable the wizard (around line 128)
#WIZARD=off
WIZARD=on
I'm currently following the instructions here
to build tensorflow from source using bazel.
After setting up the configuration, and attempting to build it, I get this error:
Cuda Configuration Error: Error reading C:/Program Files/NVIDIA GPU
Computing To olkit/CUDA/v9.0/include/cudnn.h: java.io.IOException:
ERROR: src/main/native/win dows/processes-jni.cc(239):
CreateProcessW("grep" --color=never -A1 -E "#define CUDNN_MAJOR"
"C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v9.0/include/cu
dnn.h"): Das System kann die angegebene Datei nicht finden.
The last phrase translates to "no such file or directory".
But I'm 100% sure I installed cuDNN 7.1.2 correctly, merging the downloaded bin/include/lib folder's with the preexisting CUDA folders. If I copy/paste the path from the error message, there it is cudnn.h! I also run everything in administator etc..
This problem shows up a few times on google, linking it to a mis-configured theano setup, but I'm not using theano right now.
Why doesn't bazel find the file, when it's definitely there?
EDIT: I would also be very thankful if anyone has a link a pre-built version of tensorflow for CUDA compute capability 3.0!
Thank you in advance!
The error indicated that grep.exe can't be found. I tried grep for Windows and msys2. Both will do.
While trying to install Tensorflow on my Raspberry Pi 3B as part of the g2p-seq2seq program I've run into a bit of an issue.
Using the guide here, I run into an error when executing the command:
bazel build -c opt --copt="-mfpu=neon" --local_resources 1024,1.0,1.0 --verbose_failures tensorflow/tools/pip_package:build_pip_package
I get the following error:
WARNING: Sandboxed execution is not supported on your system and thus hermeticity of actions cannot be guaranteed. See http://bazel.io/docs/bazel-user-manual.html#sandboxing for more information. You can turn off this warning via --ignore_unsupported_sandboxing.
ERROR: /home/pi/makevoicedemo/tf/tensorflow/tensorflow/tensorflow.bzl:571:26: Traceback (most recent call last):
File "/home/pi/makevoicedemo/tf/tensorflow/tensorflow/tensorflow.bzl", line 565
rule(attrs = {"srcs": attr.label_list..."), <3 more arguments>)}, <2 more arguments>)
File "/home/pi/makevoicedemo/tf/tensorflow/tensorflow/tensorflow.bzl", line 571, in rule
attr.label_list(cfg = "data", allow_files = True)
expected ConfigurationTransition or NoneType for 'cfg' while calling label_list but got string instead: data.
ERROR: com.google.devtools.build.lib.packages.BuildFileContainsErrorsException: error loading package '': Extension file 'tensorflow/tensorflow.bzl' has errors.
INFO: Elapsed time: 0.337s
I know the Warning notice is not that big of an issue, however I don't know how to fix the two Errors following that. The documentation I found for Tensorflow on Raspberry Pi regarding this issue is difficult to follow. If anyone has any advice I would appreciate it.
Sorry you're hitting problems! The errors looks like a bug, so could you file this over at https://github.com/tensorflow/tensorflow/issues?
I'm failing to compiled the rabbitmq-c library on Mac OS 10.6.6
I intend to build the php-ampq extension against it.
I've tried both the latest branch of rabbitmq-c and rabbitmq-codegen according to the instructions here and the specific branches according to the instructions here.
Running autoreconf -i as per instructions I get:
glibtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.ac and
glibtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
glibtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
configure.ac:12: installing `./config.sub'
configure.ac:12: required file `./ltmain.sh' not found
configure.ac:3: installing `./missing'
configure.ac:3: installing `./install-sh'
configure.ac:12: installing `./config.guess'
examples/Makefile.am: installing `./depcomp'
autoreconf: automake failed with exit status: 1
Running simply autoconf I get:
configure.ac:3: error: possibly undefined macro: AM_INIT_AUTOMAKE
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
configure.ac:12: error: possibly undefined macro: AM_PROG_LIBTOOL
configure.ac:90: error: possibly undefined macro: AM_CONDITIONAL
Most of what I can find by searching online suggests I don't have libtool or automake. I have both.
I'm afraid I'm out of my depth with autoconf, so I don't know how/where to alter configure.ac, or whether the warning is anything do with the missing ltmain.sh file.
I solved the same problem by installing pkg-config:
sudo port install pkgconfig