MulticoreTSNE on python 3.7.3 using conda about multicore-tsne HOT 3 OPEN

I was able to get multicore tsne on python 3.7 if you're running it on windows, you'll need to follow the instructions here in order to get it working.

from multicore-tsne.

Sorry for the radio silence; I have been trying to find out what is happening. In the end I feel this is not a problem with multicoreTSNE itself but other software I need for its installation.

I am a Mac user, and also tried to install MulticoreTSNE on linux based hpc. In both, I get an error message (long) which makes me think that something is wrong with my cmake or similar. I can use it to install other packages that require cmake, and the version seems to be alright

ending with either of the following:

$ pip install multicoreTSNE
or
$ git clone https://github.com/DmitryUlyanov/Multicore-TSNE.git
$ cd Multicore-TSNE/
$ pip install .

ERROR: Command "/anaconda3/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/qq/sgxv2d656r3c49k_bp0l696w0000gn/T/pip-install-tobo8p_u/multicoreTSNE/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/qq/sgxv2d656r3c49k_bp0l696w0000gn/T/pip-record-uux_cqpb/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/qq/sgxv2d656r3c49k_bp0l696w0000gn/T/pip-install-tobo8p_u/multicoreTSNE/

and includes

_cmake version 3.13.3

CMake suite maintained and supported by Kitware (kitware.com/cmake).
-- The CXX compiler identification is Clang 4.0.1
-- Check for working CXX compiler: /anaconda3/bin/x86_64-apple-darwin13.4.0-clang++
-- Check for working CXX compiler: /anaconda3/bin/x86_64-apple-darwin13.4.0-clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) (Required is at least version "2")
-- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND) (Required is at least version "2")
CMake Warning at CMakeLists.txt:22 (MESSAGE):
  Not using OpenMP.  Performance will suffer._

When I use
$ python setup.py install
The result is a bit different, ending with

_clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [CMakeFiles/tsne_multicore.dir/build.make:102: /Users/onurbasak/Documents/2_Hpc_sequencing/software/Multicore-TSNE/build/lib.macosx-10.9-x86_64-3.7/MulticoreTSNE/libtsne_multicore.so] Error 1
make[2]: Leaving directory '/Users/onurbasak/Documents/2_Hpc_sequencing/software/Multicore-TSNE/build/temp.macosx-10.9-x86_64-3.7'
make[1]: *** [CMakeFiles/Makefile2:76: CMakeFiles/tsne_multicore.dir/all] Error 2
make[1]: Leaving directory '/Users/onurbasak/Documents/2_Hpc_sequencing/software/Multicore-TSNE/build/temp.macosx-10.9-x86_64-3.7'
make: *** [Makefile:87: all] Error 2

ERROR: Cannot find make? See above errors._

I am sure I have cmake, clang etc. but there might be a path problem... I will go through this with a specialist

I also tried the conda version, but couldnt make it work. The version of python for this seems to be <3.7.0:

$ conda search multicore-tsne --info

...
_multicore-tsne 0.1_d4ff4aab py36h3e44d54_0

file name : multicore-tsne-0.1_d4ff4aab-py36h3e44d54_0.tar.bz2
name : multicore-tsne
version : 0.1_d4ff4aab
build : py36h3e44d54_0
build number: 0
size : 70 KB
license : BSD-3-Clause
subdir : linux-64
url : https://conda.anaconda.org/conda-forge/linux-64/multicore-tsne-0.1_d4ff4aab-py36h3e44d54_0.tar.bz2
md5 : f14137001befebcea0988f12633f1dda
timestamp : 2018-11-12 17:04:10 UTC
dependencies:

• cffi >=1.11.5
• libstdcxx-ng >=4.9
• numpy >=1.9.3,<2.0a0
• python >=3.6,<3.7.0a0_

$ python --version
Python 3.7.3

from multicore-tsne.

Ok, the issue is solved.

My conda crushed during an update, which lead me to reinstall miniconda and mange my environments a bit better. I could install MulticoreTSNE for python 3.7.3 following 'git clone...'. The conda version (conda install -c conda-forge multicore-tsne) installed in 3.6.8 my failed in 3.7.3 in my hands.

Overall this was either due to the presence of too many packages in the env, or something that was corrupted (or paths lost) on the way.

Sorry to bother with a none multicoreTSNE related issue

from multicore-tsne.