Re: Get an error message when trying to install sage cell server

[leif]

Aaron E-J wrote:
> I am interested in contributing to the sage cell server and am going through the steps outlined in
> the readme in the https://github.com/sagemath/sagecell#id1">github page. When I get to step #5, I
> get the following error message that is detailed below.

FWIW, you already failed in step 2 ("Compile Sage 5.8") ... ;-)

You grabbed a binary distribution of Sage *5.9*, which was released
*after* the sagecell spkg you're trying to install, so it's not too
surprising that the patches no longer apply.

So either retry with Sage 5.8, or wait for more helpful replies ...

(I *think* a binary distribution might work as well, but I'm not sure.)


-leif


> I am running this on a kubuntu virtual machine (VMWare) but I don't see that should matter. Is there another way to achieve this? Can I just download and unzip the archive? If this is the case, where do I unzip it to? Any insight as to what the issue might be is greatly appreciated, thanks!
>
> aaronej@ubuntu:~/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux$ ./sage -i http://sage.math.washington.edu/home/jason/sagecell-spkg/sagecell-2013-04-05.spkg
> Attempting to download package sagecell-2013-04-05
>>>> Downloading sagecell-2013-04-05.spkg.
> [............................................................]
> sagecell-2013-04-05
> ====================================================
> Extracting package /home/aaronej/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/spkg/optional/sagecell-2013-04-05.spkg
> -rw-rw-r-- 1 aaronej aaronej 60793713 May 18 17:36 /home/aaronej/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/spkg/optional/sagecell-2013-04-05.spkg
> Finished extraction
> ****************************************************
> Host system:
> Linux ubuntu 3.8.0-21-generic #32-Ubuntu SMP Tue May 14 22:16:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> ****************************************************
> C compiler: gcc
> C compiler version:
> Using built-in specs.
> COLLECT_GCC=gcc
> COLLECT_LTO_WRAPPER=/home/aaronej/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/local/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/lto-wrapper
> Target: x86_64-unknown-linux-gnu
> Configured with: ../src/configure --prefix=/home/buildbot/build/sage/snapperkob/snapperkob_binary/build/sage-5.9/local --with-local-prefix=/home/buildbot/build/sage/snapperkob/snapperkob_binary/build/sage-5.9/local --with-gmp=/home/buildbot/build/sage/snapperkob/snapperkob_binary/build/sage-5.9/local --with-mpfr=/home/buildbot/build/sage/snapperkob/snapperkob_binary/build/sage-5.9/local --with-mpc=/home/buildbot/build/sage/snapperkob/snapperkob_binary/build/sage-5.9/local --with-system-zlib --disable-multilib --disable-nls
> Thread model: posix
> gcc version 4.7.2 (GCC)
> ****************************************************
> Patching Sage
> adding 01-sage-embedded.patch to series file
> applying 01-sage-embedded.patch
> patching file sage/misc/hg.py
> Hunk #1 succeeded at 74 with fuzz 1 (offset 0 lines).
> patching file sage/misc/sagedoc.py
> Hunk #1 FAILED at 35
> 1 out of 3 hunks FAILED -- saving rejects to file sage/misc/sagedoc.py.rej
> patching file sage/misc/sageinspect.py
> Hunk #1 FAILED at 127
> 1 out of 3 hunks FAILED -- saving rejects to file sage/misc/sageinspect.py.rej
> patching file sage/misc/session.pyx
> Hunk #1 succeeded at 67 with fuzz 1 (offset 1 lines).
> Hunk #3 FAILED at 340
> 1 out of 3 hunks FAILED -- saving rejects to file sage/misc/session.pyx.rej
> patch failed, unable to continue (try -v)
> patch failed, rejects left in working dir
> errors during apply, please fix and refresh 01-sage-embedded.patch
> Error pushing patch 01-sage-embedded.patch.
>
> real 0m3.161s
> user 0m0.976s
> sys 0m0.932s
> ************************************************************************
> Error installing package sagecell-2013-04-05
> ************************************************************************
> Please email sage-devel (http://groups.google.com/group/sage-devel)
> explaining the problem and including the relevant part of the log file
> /home/aaronej/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/logs/pkgs/sagecell-2013-04-05.log
> Describe your computer, operating system, etc.
> If you want to try to fix the problem yourself, *don't* just cd to
> /home/aaronej/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/spkg/build/sagecell-2013-04-05 and type 'make' or whatever is appropriate.
> Instead, the following commands setup all environment variables
> correctly and load a subshell for you to debug the error:
> (cd '/home/aaronej/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/spkg/build/sagecell-2013-04-05' && '/home/aaronej/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/sage' --sh)
> When you are done debugging, you can type "exit" to leave the subshell.
> ************************************************************************

--
() The ASCII Ribbon Campaign
/\ Help Cure HTML E-Mail

[Jason Grout]

On 5/19/13 7:39 PM, leif wrote:
> Aaron E-J wrote:
>> I am interested in contributing to the sage cell server and am going
>> through the steps outlined in
>> the readme in the https://github.com/sagemath/sagecell#id1">github
>> page. When I get to step #5, I
>> get the following error message that is detailed below.
>
> FWIW, you already failed in step 2 ("Compile Sage 5.8") ... ;-)
>
> You grabbed a binary distribution of Sage *5.9*, which was released
> *after* the sagecell spkg you're trying to install, so it's not too
> surprising that the patches no longer apply.
>
> So either retry with Sage 5.8, or wait for more helpful replies ...

I just updated the sagecell spkg to work with 5.9:

http://boxen.math.washington.edu/home/jason/sagecell-spkg/sagecell-2013-05-20.spkg

You might need to pop the previous patches applied with your previous
attempt (or alternatively, you can delete the sage directory and start
fresh):

cd
/home/aaronej/sage/sage-5.9-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/devel/sage
hg qpop -a
hg qdelete 01-sage-embedded.patch

Then try installing the above spkg. I'm not sure if it will work with a
binary distribution---I don't think I've ever tried it.

Thanks,

Jason

[Niles Johnson]

I've tried the sagecell-2013-05-20.spkg with a freshly compiled Sage 5.9, but still get an error.  The patches apply, but zeromq does not install.  Looking at the end of the output, I guess I need to install uuid-dev . . . 

...

Installing zeromq

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /bin/mkdir -p

checking for gawk... gawk

checking whether make sets $(MAKE)... yes

...

checking for pthread_create in -lpthread... yes

checking for sem_init in -lrt... yes

checking for uuid_generate in -luuid... no

configure: error: cannot link with -luuid, install uuid-dev.

Error configuring zeromq.

[Jason Grout]

On 5/21/13 12:00 PM, Niles Johnson wrote:
> I've tried the sagecell-2013-05-20.spkg with a freshly compiled Sage
> 5.9, but still get an error. The patches apply, but zeromq does not
> install. Looking at the end of the output, I guess I need to install
> uuid-dev . . .

Yep. Step 1 in the readme: https://github.com/sagemath/sagecell

1. Make sure you have git; if you're on Ubuntu, you�ll also need the
uuid-dev package installed (for �MQ).


Thanks,

Jason

[Aaron E-J]

Installing using the binary download version of sage does not work, gives a "cannot find such and such file" message.  Am trying it with the source version now.

On Sunday, May 19, 2013 6:03:12 PM UTC-4, Aaron E-J wrote:

I am interested in contributing to the sage cell server and am going through the steps outlined in the readme in the https://github.com/sagemath/sagecell#id1">github page. When I get to step #5, I get the following error message that is detailed below. I am running this on a kubuntu virtual machine (VMWare) but I don't see that should matter. Is there another way to achieve this? Can I just download and unzip the archive? If this is the case, where do I unzip it to? Any insight as to what the issue might be is greatly appreciated, thanks!

[Niles Johnson]

On Tuesday, May 21, 2013 1:25:10 PM UTC-4, Jason Grout wrote:

1. Make sure you have git; if you're on Ubuntu, you�ll also need the
uuid-dev package installed (for �MQ).

Ouch!  I'm on RedHat, not Ubuntu, but I guess I should have noticed that anyway . . . 

[Jason Grout]

On 5/21/13 12:54 PM, Niles Johnson wrote:
>
>
> On Tuesday, May 21, 2013 1:25:10 PM UTC-4, Jason Grout wrote:
>
>

> 1. Make sure you have git; if you're on Ubuntu, you�ll also need the
> uuid-dev package installed (for �MQ).

>
>
>
> Ouch! I'm on RedHat, not Ubuntu, but I guess I should have noticed that
> anyway . . .

Just 1 minute ago, I ran into the same problem on redhat (well, CentOS) :).

And apparently 'yum install uuid-devel' didn't work, so I'm debugging it
right now.

I'm moving the official sage cell server to CentOS, and I've been
working on setting up automated installation for the virtual machines.

Thanks,

Jason

[Niles Johnson]

On Tuesday, May 21, 2013 1:56:41 PM UTC-4, Jason Grout wrote:

I'm moving the official sage cell server to CentOS, and I've been
working on setting up automated installation for the virtual machines.

This sounds like it would be very useful for me too -- thanks for looking into it :) 

[Jason Grout]

From
http://stackoverflow.com/questions/6948032/problem-installing-zmq-on-amazon-linux-unable-to-find-uuid

yum install libuuid-devel

Thanks,

Jason

[Jason Grout]

You can see my current scratch work here, based in part on Volker's sage
notebook configuration files:

https://github.com/jasongrout/sagecell/tree/vm/contrib/vm

Thanks,

Jason

[Aaron E-J]

So I've finally had a change to get back to working on trying to install sage sell.  I've got everything set, only I'm getting the following error that makes me think I'm missing a dependency:

config.status: executing libtool commands
Making all in src
make[1]: Entering directory `/home/aaronej/sage/spkg/build/sagecell-2013-05-20/src/zeromq-2.2.0/src'
make  all-am
make[2]: Entering directory `/home/aaronej/sage/spkg/build/sagecell-2013-05-20/src/zeromq-2.2.0/src'
  CXX    libzmq_la-clock.lo
  CXX    libzmq_la-command.lo
  CXX    libzmq_la-ctx.lo
  CXX    libzmq_la-connect_session.lo
  CXX    libzmq_la-decoder.lo
  CXX    libzmq_la-device.lo
  CXX    libzmq_la-devpoll.lo
  CXX    libzmq_la-dist.lo
  CXX    libzmq_la-encoder.lo
  CXX    libzmq_la-epoll.lo
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:222:0,
                 from /usr/include/x86_64-linux-gnu/sys/epoll.h:22,
                 from epoll.cpp:25:
/usr/include/x86_64-linux-gnu/sys/sysmacros.h:32:36: error: ISO C++ 1998 does not support 'long long' [-Werror=long-long]
/usr/include/x86_64-linux-gnu/sys/sysmacros.h:35:36: error: ISO C++ 1998 does not support 'long long' [-Werror=long-long]
/usr/include/x86_64-linux-gnu/sys/sysmacros.h:38:1: error: ISO C++ 1998 does not support 'long long' [-Werror=long-long]
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:270:0,
                 from /usr/include/x86_64-linux-gnu/sys/epoll.h:22,
                 from epoll.cpp:25:
/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h:135:19: error: ISO C++ 1998 does not support 'long long' [-Werror=long-long]
/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h:136:19: error: ISO C++ 1998 does not support 'long long' [-Werror=long-long]
/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h:137:19: error: ISO C++ 1998 does not support 'long long' [-Werror=long-long]
/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h:143:17: error: ISO C++ 1998 does not support 'long long' [-Werror=long-long]
cc1plus: all warnings being treated as errors
make[2]: *** [libzmq_la-epoll.lo] Error 1
make[2]: Leaving directory `/home/aaronej/sage/spkg/build/sagecell-2013-05-20/src/zeromq-2.2.0/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/aaronej/sage/spkg/build/sagecell-2013-05-20/src/zeromq-2.2.0/src'
make: *** [all-recursive] Error 1
Error building zeromq.

real    1m22.230s
user    0m35.632s
sys     0m20.232s
************************************************************************
Error installing package sagecell-2013-05-20

************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file

  /home/aaronej/sage/logs/pkgs/sagecell-2013-05-20.log

Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to

/home/aaronej/sage/spkg/build/sagecell-2013-05-20 and type 'make' or whatever is appropriate.

Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:

  (cd '/home/aaronej/sage/spkg/build/sagecell-2013-05-20' && '/home/aaronej/sage/sage' --sh)

[Aaron E-J]

Oh, and I have git and uuid-dev so it must be something else

[Aaron E-J]

As a test, I attempted to install a standalone version of ZeroMQ but got the following message:
...
  CXXLD  test_timeo
make[1]: Leaving directory `/home/aaronej/Downloads/zeromq-3.2.3/tests'
make[1]: Entering directory `/home/aaronej/Downloads/zeromq-3.2.3'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/home/aaronej/Downloads/zeromq-3.2.3'
Making install in src
make[1]: Entering directory `/home/aaronej/Downloads/zeromq-3.2.3/src'
make[2]: Entering directory `/home/aaronej/Downloads/zeromq-3.2.3/src'
test -z "/usr/local/lib" || /bin/mkdir -p "/usr/local/lib"
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libzmq.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libzmq.so.3.0.0 /usr/local/lib/libzmq.so.3.0.0
/usr/bin/install: cannot create regular file '/usr/local/lib/libzmq.so.3.0.0': Permission denied
make[2]: *** [install-libLTLIBRARIES] Error 1
make[2]: Leaving directory `/home/aaronej/Downloads/zeromq-3.2.3/src'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/aaronej/Downloads/zeromq-3.2.3/src'
make: *** [install-recursive] Error 1

[Jason Grout]

On 5/27/13 11:36 AM, Aaron E-J wrote:
> So I've finally had a change to get back to working on trying to install

> sage sell.I've got everything set, only I'm getting the following error

> that makes me think I'm missing a dependency:

I think it's the error that is solved on this ticket for the sage zmq spkg:

http://trac.sagemath.org/sage_trac/ticket/14518

Can you try doing

export LIBZMQ_EXTRA_CXXFLAGS="${LIBZMQ_EXTRA_CXXFLAGS} -Wno-long-long "

in the shell before installing the sage cell? If I understand
http://travlr.github.io/zmqirclog/101112.html correctly, that should set
the correct flag when compiling zeromq.

Thanks,

Jason

[Aaron E-J]

This seems to have done the trick!  Thanks a lot, I can now go enjoy the nice Memorial Day weather without it nagging me :-)

[Aaron E-J]

Hmmm... I can't figure out how to set up the SSH settings.  Sorry if this sound naïve, but what should I put for the host and username?  This is the stack trace when I try to run ../../sage web_server.py :

Traceback (most recent call last):
  File "web_server.py", line 29, in <module>
    import handlers
  File "/home/aaronej/sage/devel/sagecell-main/handlers.py", line 4, in <module>
    import tornado.websocket
  File "/home/aaronej/sage/local/lib/python2.7/site-packages/tornado-3.0.1-py2.7.egg/tornado/websocket.py", line 39, in <module>
    from tornado.netutil import Resolver
  File "/home/aaronej/sage/local/lib/python2.7/site-packages/tornado-3.0.1-py2.7.egg/tornado/netutil.py", line 25, in <module>
    import ssl
  File "/home/aaronej/sage/local/lib/python/ssl.py", line 60, in <module>
    import _ssl             # if we can't import it, let the error propagate
ImportError: No module named _ssl

[leif]

Aaron E-J wrote:
> Hmmm... I can't figure out how to set up the SSH settings.Sorry if this

> sound na�ve, but what should I put for the host and username?This is the

> stack trace when I try to run ../../sage web_server.py :
>
> Traceback (most recent call last):
> File "web_server.py", line 29, in <module>
> import handlers
> File "/home/aaronej/sage/devel/sagecell-main/handlers.py", line 4, in
> <module>
> import tornado.websocket
> File
> "/home/aaronej/sage/local/lib/python2.7/site-packages/tornado-3.0.1-py2.7.egg/tornado/websocket.py",
> line 39, in <module>
> from tornado.netutil import Resolver
> File
> "/home/aaronej/sage/local/lib/python2.7/site-packages/tornado-3.0.1-py2.7.egg/tornado/netutil.py",
> line 25, in <module>
> import ssl
> File "/home/aaronej/sage/local/lib/python/ssl.py", line 60, in <module>
> import _ssl # if we can't import it, let the error
> propagate
> ImportError: No module named _ssl

Install OpenSSL and rebuild Python. I.e., in the VM do:

$ sudo apt-get install libssl-dev

$ ./sage -f spkg/standard/python-*


-leif

[Jason Grout]

On 5/27/13 8:39 PM, Aaron E-J wrote:
> Hmmm... I can't figure out how to set up the SSH settings.Sorry if this

> sound na�ve, but what should I put for the host and username?This is the

> stack trace when I try to run ../../sage web_server.py :
>
> Traceback (most recent call last):
> File "web_server.py", line 29, in <module>
> import handlers
> File "/home/aaronej/sage/devel/sagecell-main/handlers.py", line 4, in
> <module>
> import tornado.websocket
> File
> "/home/aaronej/sage/local/lib/python2.7/site-packages/tornado-3.0.1-py2.7.egg/tornado/websocket.py",
> line 39, in <module>
> from tornado.netutil import Resolver
> File
> "/home/aaronej/sage/local/lib/python2.7/site-packages/tornado-3.0.1-py2.7.egg/tornado/netutil.py",
> line 25, in <module>
> import ssl
> File "/home/aaronej/sage/local/lib/python/ssl.py", line 60, in <module>
> import _ssl # if we can't import it, let the error
> propagate
> ImportError: No module named _ssl

Install openssl-dev into your operating system---it's looking for the
openSSL headers. That may be all that you need to do, or you might need
to reinstall python: sage -f python

Thanks,

Jason

[Aaron E-J]

So I thought I had ssh installed but apparently not.  The two commands leif gave got rid of the ssl.py error but now I am getting a different one:

aaronej@ubuntu:~/sage/devel/sagecell$ ../../sage web_server.py
2013-05-29 16:12:32,114 sagecell:INFO starting tornado web server

Traceback (most recent call last):

  File "web_server.py", line 81, in <module>
    application = SageCellServer()
  File "web_server.py", line 58, in __init__
    kernel_timeout=kernel_timeout)
  File "/home/aaronej/sage/devel/sagecell-main/trusted_kernel_manager.py", line 43, in __init__
    comp_id = self.add_computer(comp)
  File "/home/aaronej/sage/devel/sagecell-main/trusted_kernel_manager.py", line 129, in add_computer
    client = self._setup_ssh_connection(cfg["host"], cfg["username"])
  File "/home/aaronej/sage/devel/sagecell-main/trusted_kernel_manager.py", line 87, in _setup_ssh_connection
    ssh_client.connect(host, username=username)
  File "/home/aaronej/sage/local/lib/python2.7/site-packages/paramiko-1.10.1-py2.7.egg/paramiko/client.py", line 300, in connect
    retry_on_signal(lambda: sock.connect(addr))
  File "/home/aaronej/sage/local/lib/python2.7/site-packages/paramiko-1.10.1-py2.7.egg/paramiko/util.py", line 278, in retry_on_signal
    return function()
  File "/home/aaronej/sage/local/lib/python2.7/site-packages/paramiko-1.10.1-py2.7.egg/paramiko/client.py", line 300, in <lambda>
    retry_on_signal(lambda: sock.connect(addr))
  File "/home/aaronej/sage/local/lib/python/socket.py", line 226, in meth
    return getattr(self._sock,name)(*args)
socket.error: [Errno 111] Connection refused

Can you tell me if this config will work (modified lines below)?  I'm still not sure if I have the correct values.

My thinking is that it has to do with what I'm putting for the username in the config.py file.  What should I put?  I've tried "aaronej@localhost", localhost and simply "" to no success.  Leaving it as None does not work either.

On Monday, May 27, 2013 11:33:08 PM UTC-4, leif wrote:

Aaron E-J wrote:
> Hmmm... I can't figure out how to set up the SSH settings.Sorry if this

> sound na�ve, but what should I put for the host and username?This is the

[Aaron E-J]

_default_config = {"host": "localhost",
                  "username": "aaronej@localhost",
                  "python": sage + " -python",
                  "location": os.path.dirname(os.path.abspath(__file__)),

[Jason Grout]

On 5/29/13 6:39 PM, Aaron E-J wrote:
> So I thought I had ssh installed but apparently not.The two commands

We're making progress! It now seems that you may have a firewall that
is blocking connections. To test this, try disabling your firewall
(temporarily!) to see if the error goes away.





>
> Can you tell me if this config will work (modified lines below)?I'm

> still not sure if I have the correct values.
>
> My thinking is that it has to do with what I'm putting for the username

> in the config.py file.What should I put?I've tried "aaronej@localhost",
> localhost and simply "" to no success.Leaving it as None does not work
> either.

if 'ssh aaronej@localhost' works from the user you are running the cell
server as, then that config setting is fine.

Thanks,

Jason