fatal error: gsl/gsl_rng.h: No such file or directory

Question

fatal error: gsl/gsl_rng.h: No such file or directory

xnfei opened this issue 5 years ago · comments

Could anyone help? When I tried to run this project in Ubuntu 18.04, I faced this problem:

./apf/base/allocate.c:632:10: fatal error: gsl/gsl_rng.h: No such file or directory
#include "gsl/gsl_rng.h"
^~~~~~~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
Makefile:2: recipe for target 'all' failed
make: *** [all] Error 1

Aaron Schein commented 4 years ago

No rush!

Aaron Schein · Answer 1 · Thu Feb 27 2020 03:58:53 GMT+0800 (China Standard Time)

Have you installed GNU Scientific Library (GSL)?

Aaron Schein · Answer 2 · Thu Feb 27 2020 12:45:28 GMT+0800 (China Standard Time)

Hi Bill,

I don’t understand your message. Have you installed GSL and successfully compiled the code?

xnfei · Answer 3 · Thu Feb 27 2020 22:17:16 GMT+0800 (China Standard Time)

Yes, I have installed GSL and successfully compiled the setup.py. But I don’t know how to run experiments or tests. There is no instructions I could follow, so I don’t know what to do next. Bill

…

On Wed, Feb 26, 2020 at 10:45 PM Aaron Schein ***@***.***> wrote: Hi Bill, I don’t understand your message. Have you installed GSL and successfully compiled the code? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AOG47T4NXEOAKTII5LM2TG3RE5AOTA5CNFSM4K4LSBP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENC5D6Q#issuecomment-591778298>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOG47T7SXJ3ZY33H2FR74ULRE5AOTANCNFSM4K4LSBPQ> .

xnfei · Answer 4 · Fri Feb 28 2020 02:39:29 GMT+0800 (China Standard Time)

I think I have installed GSL, but I don't know how to check if it's installed successfully.
I did as below, following this reference：https://coral.ise.lehigh.edu/jild13/2016/07/11/hello/

wget ftp://ftp.gnu.org/gnu/gsl/gsl-*.*.tar.gz
tar -zxvf gsl-..tar.gz
cd gsl-1.7
mkdir /home/yourname/gsl
./configure --prefix=/home/yourname/gsl
make
make check
make install

Aaron Schein · Answer 5 · Fri Feb 28 2020 03:36:00 GMT+0800 (China Standard Time)

Hi Bill,

There are tests and experiment scripts in the src directory. But, I am happy to write a Jupyter Notebook that shows how to use the model; I can do that this weekend.

In the meantime, can you type "Make" into the terminal and copy-and-paste the output?

Best,
Aaron

Aaron Schein · Answer 6 · Fri Feb 28 2020 03:55:34 GMT+0800 (China Standard Time)

Your messages appear to be corrupted. Can you log-in to Github from a browser and double-check that your messages are written as intended? I am seeing lots of HTML (which I don't think is the output of Make).

xnfei · Answer 7 · Fri Feb 28 2020 03:58:20 GMT+0800 (China Standard Time)

It shows:
xiaoning@DESKTOP-DMOUKTE:$ make
make: *** No targets specified and no makefile found. Stop.
xiaoning@DESKTOP-DMOUKTE:$ cd venv/prgds-master/src/
xiaoning@DESKTOP-DMOUKTE:/venv/prgds-master/src$ make
python3 setup.py build_ext -i
running build_ext
xiaoning@DESKTOP-DMOUKTE:/venv/prgds-master/src$

Aaron Schein · Answer 8 · Fri Feb 28 2020 04:03:20 GMT+0800 (China Standard Time)

In the src directory, please try typing

python tests/test_prgds.py

and tell me what happens.

xnfei · Answer 9 · Fri Feb 28 2020 04:05:57 GMT+0800 (China Standard Time)

I tried both python and python3.

xiaoning@DESKTOP-DMOUKTE:~/venv/prgds-master/src$ python3 tests/test_prgds.py
Traceback (most recent call last):
File "tests/test_prgds.py", line 4, in
from apf.models.prgds import PRGDS
ImportError: /usr/lib/x86_64-linux-gnu/libgsl.so.23: undefined symbol: cblas_ctrmv

xiaoning@DESKTOP-DMOUKTE:~/venv/prgds-master/src$ python tests/test_prgds.py
Traceback (most recent call last):
File "tests/test_prgds.py", line 4, in
from apf.models.prgds import PRGDS
ImportError: No module named prgds

Aaron Schein · Answer 10 · Fri Feb 28 2020 04:17:34 GMT+0800 (China Standard Time)

Looks like it didn't compile properly. Can you switch to the src directory and remove the build
rm -rf build
and then type Make again and paste the first few lines.

xnfei · Answer 11 · Fri Feb 28 2020 04:49:37 GMT+0800 (China Standard Time)

well, it shows the same:

xiaoning@DESKTOP-DMOUKTE:/venv/prgds-master/src$ rm -rf build
xiaoning@DESKTOP-DMOUKTE:/venv/prgds-master/src$ make
python3 setup.py build_ext -i
running build_ext
xiaoning@DESKTOP-DMOUKTE:~/venv/prgds-master/src$

xnfei · Answer 12 · Fri Feb 28 2020 07:57:38 GMT+0800 (China Standard Time)

Any advice, sir?

Aaron Schein · Answer 13 · Fri Feb 28 2020 08:05:02 GMT+0800 (China Standard Time)

Hi Bill,

I just tried cloning the repo on a Linux machine and compiling. Here's the output I got:

python setup.py build_ext -i
Compiling ./apf/base/allocate.pyx because it changed.
Compiling ./apf/base/apf.pyx because it changed.
Compiling ./apf/base/bessel.pyx because it changed.
Compiling ./apf/base/conf_hypergeom.pyx because it changed.
Compiling ./apf/base/cyutils.pyx because it changed.
Compiling ./apf/base/mcmc_model_parallel.pyx because it changed.
Compiling ./apf/base/sample.pyx because it changed.
Compiling ./apf/base/sbch.pyx because it changed.
Compiling ./apf/models/gpdptf.pyx because it changed.
Compiling ./apf/models/pgds.pyx because it changed.
Compiling ./apf/models/prgds.pyx because it changed.
[ 1/11] Cythonizing ./apf/base/allocate.pyx
[ 2/11] Cythonizing ./apf/base/apf.pyx
[ 3/11] Cythonizing ./apf/base/bessel.pyx
[ 4/11] Cythonizing ./apf/base/conf_hypergeom.pyx
[ 5/11] Cythonizing ./apf/base/cyutils.pyx
[ 6/11] Cythonizing ./apf/base/mcmc_model_parallel.pyx
[ 7/11] Cythonizing ./apf/base/sample.pyx
[ 8/11] Cythonizing ./apf/base/sbch.pyx
[ 9/11] Cythonizing ./apf/models/gpdptf.pyx
[10/11] Cythonizing ./apf/models/pgds.pyx
[11/11] Cythonizing ./apf/models/prgds.pyx
running build_ext

I'm not sure why you're not seeing the same thing. Perhaps you haven't installed Cython?

xnfei · Answer 14 · Fri Feb 28 2020 08:09:26 GMT+0800 (China Standard Time)

I already got this [ 1/11] Cythonizing stuff.
I guess after the first time compling , I would simply see

python3 setup.py build_ext -i
running build_ext

what i really want to know is what to do next

xnfei · Answer 15 · Fri Feb 28 2020 08:11:40 GMT+0800 (China Standard Time)

for example, is there any result i can see?

Aaron Schein · Answer 16 · Fri Feb 28 2020 08:16:21 GMT+0800 (China Standard Time)

OK then please do what I asked before:

cd into src and type:
python tests/test_prgds.py

And, as I stated above, I will push a Jupyter Notebook this weekend that gives a simple example of how to run the model on a data set.

xnfei · Answer 17 · Fri Feb 28 2020 08:38:48 GMT+0800 (China Standard Time)

I cloned the project and ran it again, now i have something new:

xiaoning@DESKTOP-DMOUKTE:~/venv/New folder/prgds-master/src$ python3 tests/test_prgds.py
Traceback (most recent call last):
File "tests/test_prgds.py", line 4, in
from apf.models.prgds import PRGDS
ImportError: /usr/lib/x86_64-linux-gnu/libgsl.so.23: undefined symbol: cblas_ctrmv

xnfei · Answer 18 · Sat Feb 29 2020 01:11:34 GMT+0800 (China Standard Time)

I tried again from the very first step.
Finally, I got this error:
ModuleNotFoundError: No module named 'apf.models.prgds'

xiaoning@DESKTOP-DMOUKTE:~/venv/case1/prgds-master/src$ python3 setup.py
Compiling ./apf/base/allocate.pyx because it changed.
Compiling ./apf/base/apf.pyx because it changed.
Compiling ./apf/base/bessel.pyx because it changed.
Compiling ./apf/base/conf_hypergeom.pyx because it changed.
Compiling ./apf/base/cyutils.pyx because it changed.
Compiling ./apf/base/mcmc_model_parallel.pyx because it changed.
Compiling ./apf/base/sample.pyx because it changed.
Compiling ./apf/base/sbch.pyx because it changed.
Compiling ./apf/models/gpdptf.pyx because it changed.
Compiling ./apf/models/pgds.pyx because it changed.
Compiling ./apf/models/prgds.pyx because it changed.
[ 1/11] Cythonizing ./apf/base/allocate.pyx
[ 2/11] Cythonizing ./apf/base/apf.pyx
[ 3/11] Cythonizing ./apf/base/bessel.pyx
[ 4/11] Cythonizing ./apf/base/conf_hypergeom.pyx
[ 5/11] Cythonizing ./apf/base/cyutils.pyx
[ 6/11] Cythonizing ./apf/base/mcmc_model_parallel.pyx
[ 7/11] Cythonizing ./apf/base/sample.pyx
[ 8/11] Cythonizing ./apf/base/sbch.pyx
[ 9/11] Cythonizing ./apf/models/gpdptf.pyx
[10/11] Cythonizing ./apf/models/pgds.pyx
[11/11] Cythonizing ./apf/models/prgds.pyx
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help

error: no commands supplied
xiaoning@DESKTOP-DMOUKTE:/venv/case1/prgds-master/src$ python3 tests/test_prgds.py
Traceback (most recent call last):
File "tests/test_prgds.py", line 4, in
from apf.models.prgds import PRGDS
ModuleNotFoundError: No module named 'apf.models.prgds'
xiaoning@DESKTOP-DMOUKTE:/venv/case1/prgds-master/src$

Aaron Schein · Answer 19 · Sat Feb 29 2020 02:38:20 GMT+0800 (China Standard Time)

It looks like you typed python setup.py and then got an error. You need to type python setup.py build_ext -i. You can also use the Makefile provided in the src/ directory and type Make, which will do the same thing.

After you do that, please also show me the last lines of output to confirm that it has completed compiling successfully.

xnfei · Answer 20 · Sat Feb 29 2020 02:53:23 GMT+0800 (China Standard Time)

x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/./apf/models/prgds.o -L/usr/local/lib/ -lgsl -o /home/xiaoning/venv/demo/prgds-master/src/apf/models/prgds.cpython-38-x86_64-linux-gnu.so -fopenmp
xiaoning@DESKTOP-DMOUKTE:~/venv/demo/prgds-master/src$

Aaron Schein · Answer 21 · Sat Feb 29 2020 02:54:52 GMT+0800 (China Standard Time)

Looks good. Now what happens when you cd to the src directory and type python tests/test_prgds.py?

xnfei · Answer 22 · Sat Feb 29 2020 02:55:43 GMT+0800 (China Standard Time)

it shows this:
xiaoning@DESKTOP-DMOUKTE:~/venv/demo/prgds-master/src$ python3 tests/test_prgds.py
Traceback (most recent call last):
File "tests/test_prgds.py", line 4, in
from apf.models.prgds import PRGDS
ImportError: /usr/lib/x86_64-linux-gnu/libgsl.so.23: undefined symbol: cblas_ctrmv

Aaron Schein · Answer 23 · Sat Feb 29 2020 02:57:55 GMT+0800 (China Standard Time)

This suggests there's some problem finding the header files for your installation of GSL. Are you using Anaconda?

Aaron Schein · Answer 24 · Sat Feb 29 2020 03:00:08 GMT+0800 (China Standard Time)

There are instructions at the bottom of the ReadMe for how to use Anaconda to install GCC and GSL. If you install GCC/GSL a different way, you may have to troubleshoot linking those libraries/headers.

xnfei · Answer 25 · Sat Feb 29 2020 03:00:24 GMT+0800 (China Standard Time)

No, in Ubuntu, I directly installed python

Aaron Schein · Answer 26 · Sat Feb 29 2020 03:01:51 GMT+0800 (China Standard Time)

You can install Anaconda on Ubuntu. Please try that.

xnfei · Answer 27 · Sat Feb 29 2020 03:02:15 GMT+0800 (China Standard Time)

okay , let me try.

xnfei · Answer 28 · Sat Feb 29 2020 03:09:09 GMT+0800 (China Standard Time)

I have a lecture from1:30 to 4:15p.m.
please allow me to reponse later

xnfei · Answer 29 · Mon Mar 02 2020 11:36:36 GMT+0800 (China Standard Time)

Yeah! It seems I could successfully run this command : python tests/test_prgds.py
But I also got this Error. May I ask what does this mean?

Traceback (most recent call last):
File "apf/base/apf.pyx", line 217, in apf.base.apf.APF.reconstruct
return tl.kruskal_to_tensor(mtxs, weights=self.core_Q)[subs]
TypeError: kruskal_to_tensor() got an unexpected keyword argument 'weights'
Exception ignored in: 'apf.base.apf.APF._update_Y_PQ'
Traceback (most recent call last):
File "apf/base/apf.pyx", line 217, in apf.base.apf.APF.reconstruct
return tl.kruskal_to_tensor(mtxs, weights=self.core_Q)[subs]
TypeError: kruskal_to_tensor() got an unexpected keyword argument 'weights'

xnfei · Answer 30 · Mon Mar 02 2020 12:05:40 GMT+0800 (China Standard Time)

When I tried to run python tests/test_pgds.py
It returned:

Exception ignored in: 'apf.base.apf.APF._update_Y_PQ'
Traceback (most recent call last):
File "/home/xiaoning/anaconda3/lib/python3.7/site-packages/numpy/ma/core.py", line 2863, in new
raise MaskError(msg % (nd, nm))
numpy.ma.core.MaskError: Mask and data not compatible: data size is 1, mask size is 36.

Aaron Schein · Answer 31 · Mon Mar 02 2020 22:42:05 GMT+0800 (China Standard Time)

OK, this is progress.

It looks like the Python library Tensorly updated since I wrote this code. The old version of
tensorly.kruskal_to_tensor used to take a weights argument. The new version does not. That is annoying. I will update the code to be consistent with the latest version of Tensorly.

In the meantime, if you are in a rush, you will need to install an older version of Tensorly (0.4.2). You can do that with Anaconda by typing:

conda install -c conda-forge tensorly=0.4.2

Aaron Schein · Answer 32 · Mon Mar 02 2020 23:45:52 GMT+0800 (China Standard Time)

Also, please pull. I fixed a naming inconsistency between the model files and the test scripts.

xnfei · Answer 33 · Tue Mar 03 2020 00:42:19 GMT+0800 (China Standard Time)

I used your new scripts, but it returned the same.
so I reinstall the tensorly. Finally!

(base) xiaoning@DESKTOP-DMOUKTE:~/venv/demo/prgds-master/src$ python tests/test_prgds.py
Using numpy backend.
seed: 8496
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