Installation issues

[sgold...@wisc.edu]

Hi,

I just successfully installed dedalus on Ubuntu 16.04.1 LTS.

I had these issues to overcome:

1. pip3 doesn't seem to be part of the Python 3.5.1 distro that install.sh installs. Or at least pip3 did not get installed in my dedalus directory.

Symptom:

install.sh: line 692: /staff/sgoldstein/Projects/Dedalus/dedalus/bin/pip3: No such file or directory

********************************************
********************************************
Failure. Check /staff/sgoldstein/Projects/Dedalus/dedalus/dedalus_install.log. The last 10 lines are above.

Fix:
Copy a pip3 python script to the bin directory (and maybe change the #! line to call the dedalus python3 binary).

2. The current version of install.sh installs Python 3.5.1, but the PYTHONPATH envar points to python3.4.

$ grep -n python3.4 install.sh
585:export PYTHONPATH=${DEST_DIR}/lib/python3.4/site-packages/

Symptom:
None for what I'veI tried so. I guess the packages in lib/python3.5/site-packages can be found elsewhere.

Fix: Edit this line in install.sh or the lines in activate and activate.csh.

[Jeffrey S. Oishi]

Hi,

Thanks for writing and reporting these issues!

First, I just tried the current install script on a fresh Ubuntu 16.04.1 install. It appears that the script works correctly (building pip3 and using it) if you install all of the packages suggested by the install script (see here:https://bitbucket.org/dedalus-project/dedalus/src/de7c0146ebc1a196574fe35f9675a3d36d98eb93/docs/install.sh?at=default&fileviewer=file-view-default#install.sh-346). I think the problem in your case might be that you don't have the SSL headers installed, in which case Python cannot build its ssl module. When the ssl module doesn't build, pip doesn't build. If you could try seeing if you have the ssl headers installed (libssl-dev is the Ubuntu package), that would be helpful in tracking down if this is another bug.

As for the second error you point out, that is absolutely a bug! I've pushed a fix to the install script. Thank you for the catch.

Please let me know if you have any further problems.

thanks,

Jeff

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[Steve Goldstein]

Hi Jeff,

On 01/26/2017 02:24 PM, Jeffrey S. Oishi wrote:

 When the ssl module doesn't build, pip doesn't build. If you could try seeing if you have the ssl headers installed (libssl-dev is the Ubuntu package), that would be helpful in tracking down if this is another bug.

I'm not sure how to rigorously answer that.    I'll paste in the results of running "locate libssl"  and "locate libssl-dev".

I did execute the "sudo apt-get install ... libssl-dev ..." command, but it's entirely possible that it is missing --- If it was installed in /usr/lib, our nightly updates might have wiped it out before I completed the installation.   In retrospect, I realized I should have used something like a --prefix argument for the apt-get install commands.

Thanks for your quick response,

Steve Goldstein
Research Computing Facilitator
Departments of Math and Botany
University of Wisconsin-Madison

===================================================



vv207: Dedalus$  locate libssl

/lib/x86_64-linux-gnu/libssl.so.1.0.0
/usr/lib/firefox/libssl3.so
/usr/lib/thunderbird/libssl3.so
/usr/lib/x86_64-linux-gnu/libssl.a
/usr/lib/x86_64-linux-gnu/libssl.so
/usr/lib/x86_64-linux-gnu/libssl3.so
/usr/lib/x86_64-linux-gnu/libssl3.so.1d
/usr/lib/x86_64-linux-gnu/pkgconfig/libssl.pc
/usr/local/MATLAB/R2015b/bin/glnxa64/libssl.so.1
/usr/local/MATLAB/R2015b/bin/glnxa64/libssl.so.1.0.0
/usr/local/MATLAB/R2015b/sys/jxbrowser/glnxa64/xulrunner/xulrunner-linux-64/libssl3.so
/usr/local/MATLAB/R2015b/toolbox/compiler_sdk/mps_clients/c/glnxa64/lib/libssl.so
/usr/local/MATLAB/R2015b/toolbox/compiler_sdk/mps_clients/c/glnxa64/lib/libssl.so.1
/usr/local/MATLAB/R2015b/toolbox/compiler_sdk/mps_clients/c/glnxa64/lib/libssl.so.1.0.0
/usr/local/MATLAB/R2016b/bin/glnxa64/libssl.so.1
/usr/local/MATLAB/R2016b/bin/glnxa64/libssl.so.1.0.0
/usr/local/MATLAB/R2016b/sys/jxbrowser/glnxa64/xulrunner/xulrunner-linux-64/libssl3.so
/usr/local/MATLAB/R2016b/toolbox/compiler_sdk/mps_clients/c/glnxa64/lib/libssl.so
/usr/local/MATLAB/R2016b/toolbox/compiler_sdk/mps_clients/c/glnxa64/lib/libssl.so.1
/usr/local/MATLAB/R2016b/toolbox/compiler_sdk/mps_clients/c/glnxa64/lib/libssl.so.1.0.0
/usr/share/doc/libssl-dev
/usr/share/doc/libssl1.0.0
/usr/share/doc/libssl-dev/changelog.Debian.gz
/usr/share/doc/libssl-dev/changelog.gz
/usr/share/doc/libssl-dev/copyright
/usr/share/doc/libssl1.0.0/changelog.Debian.gz
/usr/share/doc/libssl1.0.0/copyright
/var/lib/dpkg/info/libssl-dev:amd64.list
/var/lib/dpkg/info/libssl-dev:amd64.md5sums
/var/lib/dpkg/info/libssl1.0.0:amd64.list
/var/lib/dpkg/info/libssl1.0.0:amd64.md5sums
/var/lib/dpkg/info/libssl1.0.0:amd64.postinst
/var/lib/dpkg/info/libssl1.0.0:amd64.postrm
/var/lib/dpkg/info/libssl1.0.0:amd64.shlibs
/var/lib/dpkg/info/libssl1.0.0:amd64.symbols
/var/lib/dpkg/info/libssl1.0.0:amd64.templates
/var/lib/dpkg/info/libssl1.0.0:amd64.triggers

vv207: Dedalus$  locate libssl-dev

/usr/share/doc/libssl-dev
/usr/share/doc/libssl-dev/changelog.Debian.gz
/usr/share/doc/libssl-dev/changelog.gz
/usr/share/doc/libssl-dev/copyright
/var/lib/dpkg/info/libssl-dev:amd64.list
/var/lib/dpkg/info/libssl-dev:amd64.md5sums

[Jeffrey S. Oishi]

Hi Steve,

One thing you can try is to look at your failed install and see if you can do

path/to/bad_dedalus/python3 -c "import ssl"

If it returns nothing, that would tell us something else is the problem. If it returns

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named 'ssl'

Then we know that the lack of SSL headers is indeed the problem...

j

 

[Steve Goldstein]

Hi Jeff,

I wouldn't invest a lot of time in tracking this down now. I made
several attempts at the installation and made lots of mistakes so it's
not unlikely this is a "user error."

Some of the earlier attempts involved installing some of the packages in
~/.local/ and I can't guarantee that those binaries and libraries
weren't mingled in the dedalus installation.

After testing dedalus for a while, we plan to install it system wide.
When we get to that phase, I'll ask our sys admin to be on the lookup
for a potential pip3 bug.

Steve

On 01/26/2017 04:03 PM, Jeffrey S. Oishi wrote:
> Hi Steve,
>
> One thing you can try is to look at your failed install and see if you
> can do
>
> path/to/bad_dedalus/python3 -c "import ssl"
>
> If it returns nothing,

It returns nothing for both the dedalus python3 and the system version:

vv207: Dedalus$ ./dedalus/bin/python3 -c "import ssl"

vv207: Dedalus$ source ./dedalus/bin/activate

(dedalus)vv207: Dedalus$ which python3
/staff/sgoldstein/Projects/Dedalus/dedalus/bin/python3

(dedalus)vv207: Dedalus$ python3 -c "import ssl"
(dedalus)vv207: Dedalus$

(dedalus)vv207: Dedalus$ deactivate
vv207: Dedalus$ which python3
/usr/bin/python3
vv207: Dedalus$ python3 -c "import ssl"
vv207: Dedalus$

[jason.o...@gmail.com]

Good Afternoon Jeff,

I'm hoping you can help me. I'm having the same problem with pip3 failing to install. Here is the direct output:

###

Installing OPENSSL
Installing ZLIB
Installing Python.
PY_CFLAGS = -I/home/jason/dedalus/include
Installing FFTW.
pip installing cython.
********************************************
FAILURE REPORT:
********************************************

rm -rf .libs _libs
rm -f *.o
rm -f *.lo
make[1]: Leaving directory '/home/jason/dedalus/src/fftw-3.3.4/tools'
Making clean in m4
make[1]: Entering directory '/home/jason/dedalus/src/fftw-3.3.4/m4'
rm -rf .libs _libs
rm -f *.lo
make[1]: Leaving directory '/home/jason/dedalus/src/fftw-3.3.4/m4'
install.sh: line 719: /home/jason/dedalus/bin/pip3: No such file or directory

********************************************
********************************************
Failure. Check /home/jason/dedalus/dedalus_install.log. The last 10 lines are above.

###

Seeing this posting, I've checked the SSL headings

###

dedalus/bin/python3 -c "import ssl"

Traceback (most recent call last):
File "<string>", line 1, in <module>

File "/home/jason/dedalus/lib/python3.5/ssl.py", line 98, in <module>
import _ssl # if we can't import it, let the error propagate
ImportError: No module named '_ssl'

###

Thus, it seems that ssl is indeed the problem. However, I've installed SSL using Dedalus' own install script (see above). I am also on Ubuntu and have successful installed all of the dependencies listed in the install script. Any help you can provide would be extremely appreciated.

Thank you

Jason

[Jeffrey S. Oishi]

Hi Jason,

I'm a bit swamped at the moment (semester started yesterday), but if you could send along the install log, the output of 

$ lsb_release -a

and the output of 

$ apt -qq list libssl-dev

thanks,

j

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[Jason Olsthoorn]

After another round of tests I found a solution by installing the specific python-openssl package through apt-get. I'm not sure why it didn't just work with openssl installed but it seems to be up and running now. I'll let you know if I have further issues. 

Thanks for your time 

Jason 

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