Software Instllations for nsfpolardata.dyndns.org

[NSF-Polar-Cyberinfrastructure]

Please add the software you require below as well as the ports you require open for any publicly facing software you would like installed on the nsfpolardata.dyndns.org Amazon machine. Thank you

[MBoustani]

@pzimdars I am installing Conda in the machine that give us the chance to install most of python libraries we want. Can you please open a port for my project (GISCube) and let me know what is the IP and port that I can run my Django app there?

Thanks

[pzimdars]

@MBoustani Done. Please use port 9080 and IP # 54.183.226.231 (nsfpolardata.dyndns.org).

[curtislisle]

@pzimdars, I would like to perform a particular vagrant installation on the system Lewis and I are asking for your help with. Therefore, I would like the system we setup to include the following packages:

python 2.7.x vagrant 1.6.5 or similar virtualbox 4.3.16 or similar ansible 1.7.1

This is probably duplicate of information you have already received from Lewis, but when finished, I will want to access ports 9080 and 9000, so please open these ports. Thanks.

[MBoustani]

@pzimdars I get this error, is there something I do wrong in my side:

[ndeploy@nsfpolardata GISCube]$ python manage.py runserver 54.183.226.231:9080 Performing system checks... System check identified some issues:

System check identified 1 issue (0 silenced). November 03, 2014 - 13:01:37 Django version 1.7.1, using settings 'giscube.settings' Starting development server at http://54.183.226.231:9080/ Quit the server with CONTROL-C. Error: That IP address can't be assigned-to.

[curtislisle]

@pzimdars, I was able to login (Thanks @MBoustani ), but I receive a "curtislisle" is not on the sudo list". Is this something that can be fixed? Thx.

[curtislisle]

Never mind. @MBoustani showed me what Lewis had already showed me previously (ssh ndeploy). It would be great vagrant could be installed for me. I haven't used yum in a long time. I will pick this up again in a few minutes if I need to do the install myself. thanks for any help you can provide.

[curtislisle]

I performed sudo yum install ruby $ sudo yum install ruby gems $ sudo gem update --system $ sudo gem install vagrant

successfully. This installed vagrant 1.5.0, which might be too old, but nothing is needed for now. Thanks. I'll be in touch if I get stuck. I appreciate the help.

[pzimdars]

@MBoustani if the service is on localhost please use IP 172.31.3.59 port 9080.

[pzimdars]

@curtislisle no problem. Let me know if that changes or you need a newer version.

[curtislisle]

@pzimdars @lewismc I am having trouble installing virtual box to support the vagrant image on the system. VirtualBox cannot run because the kernel-devel headers installed (kernel-2.6.32-504) match only one of the two kernels configured in grub. Sadly, it is the older kernel (2.6.3-279) that is actually booted. Is there a way to reboot this system to run the kernel that matches the installed sources? vbox needs to build its driver the first time. I was hesitant to try to reboot this system without first asking you. I tried a "sudo yum update" as mentioned below, but no packages were updated. Maybe we just need to reboot now? The issue is described here:

vbox kernel and header mismatch

[lewismc]

I've installed the following for issue-85

Installed:
  mysql-server.x86_64 0:5.1.73-3.el6_5

Dependency Installed:
  mysql.x86_64 0:5.1.73-3.el6_5
  perl-DBD-MySQL.x86_64 0:4.013-3.el6
  perl-DBI.x86_64 0:1.609-4.el6

[lewismc]

I've installed the following

Installed:
  openssl-devel.x86_64 0:1.0.1e-30.el6_6.2

Dependency Installed:
  keyutils-libs-devel.x86_64 0:1.4-5.el6
  krb5-devel.x86_64 0:1.10.3-33.el6
  libcom_err-devel.x86_64 0:1.41.12-21.el6
  libselinux-devel.x86_64 0:2.0.94-5.8.el6
  libsepol-devel.x86_64 0:2.0.41-4.el6

[lewismc]

I've installed

Installed:
  python-dateutil.noarch 0:1.4.1-6.el6             python-feedparser.noarch 0:5.1.2-2.el6
  python-storm.x86_64 0:0.19-1.el6

[lewismc]

I've installed

Installed:
  mysql-devel.x86_64 0:5.1.73-3.el6_5

[pzimdars]

System rebooted. Updated to CentOS 6.6 (latest) and matching kernel.

[lewismc]

Thank you @pzimdars

[lewismc]

@pzimdars I don't want to bugger around with the Python distribution but we need it upgraded to >= 2.7. Can you please upgrade Python if possible on the machine? Thank you in advance @pzimdars

[pzimdars]

@lewismc Would this work:

[root@nsfpolardata ~]# python2.7 --version Python 2.7.3 [root@nsfpolardata ~]#

You need to call it as 'python2.7' or set an alias. Let me know.

[lewismc]

Grand, this is excellent. Thank you @pzimdars

[lewismc]

I've installed

Installed:
  python-sqlalchemy.noarch 0:0.5.5-3.el6_2

[curtislisle]

@truthkos @pzimdars Our effort to run a vagrant image on nfspolardata.dyndns.org just ran into a show stopper: vagrant usually uses VirtualBox to run boxes. For efficiency, we tried to move the pre-configured vagrant VM over, but virtualBox will not run under Zen, so this path won't work.

Advice requested: I do have a VMWare Fusion image with this software running natively. Could I request assistance to port the VMWare image over to run as an AMI? I have done this before, but would prefer to ask some experts for guidance / assistance. Is this feasible and practical?

[lewismc]

I've upgraded sqlalchemy to SQLAlchemy-0.9.8.tar.gz (4.1MB): 4.1MB downloaded

[MBoustani]

@pzimdars http://nsfpolardata.dyndns.org:9080/ stopped working today, but was working last night. Is there any thing I should do in my side?

[lewismc]

I've installed

Successfully installed mysql-python

[pzimdars]

@MBoustani System was rebooted. You need to start the service back up that you had running.

[pzimdars]

@curtislisle I assume these tools can't be built and installed on nsfpolardata instead of importing a new VM?

[curtislisle]

@pzimdars, Yes it can be built natively, but it is labor intensive, so I was l looking for alternatives. I also have a concern about tangelo services conflicting with GISCube services when they are both running natively on the same box, so the VM approach would have allowed separation. I know think I should fall back and install natively. How about setting up a new empty VM instance for me, please and sending the info. Then I will install natively on the new VM.

[pzimdars]

@curtislisle What type of resources do you need to run this? Thanks!

[lewismc]

I installed

Installed:
  R.x86_64 0:3.1.1-7.el6

Dependency Installed:
  R-core.x86_64 0:3.1.1-7.el6
  R-core-devel.x86_64 0:3.1.1-7.el6
  R-devel.x86_64 0:3.1.1-7.el6
  R-java.x86_64 0:3.1.1-7.el6
  R-java-devel.x86_64 0:3.1.1-7.el6
  blas.x86_64 0:3.2.1-4.el6
  blas-devel.x86_64 0:3.2.1-4.el6
  flac.x86_64 0:1.2.1-6.1.el6
  fontconfig-devel.x86_64 0:2.8.0-5.el6
  freetype-devel.x86_64 0:2.3.11-14.el6_3.1
  java-1.6.0-openjdk.x86_64 1:1.6.0.33-1.13.5.0.el6_6
  java-1.6.0-openjdk-devel.x86_64 1:1.6.0.33-1.13.5.0.el6_6
  java-1.7.0-openjdk.x86_64 1:1.7.0.71-2.5.3.1.el6
  jline.noarch 0:0.9.94-0.8.el6
  jpackage-utils.noarch 0:1.7.5-3.12.el6
  kpathsea.x86_64 0:2007-57.el6_2
  lapack.x86_64 0:3.2.1-4.el6
  lapack-devel.x86_64 0:3.2.1-4.el6
  libRmath.x86_64 0:3.1.1-7.el6
  libRmath-devel.x86_64 0:3.1.1-7.el6
  libX11-devel.x86_64 0:1.6.0-2.2.el6
  libXau-devel.x86_64 0:1.0.6-4.el6
  libXft-devel.x86_64 0:2.3.1-2.el6
  libXrender-devel.x86_64 0:0.9.8-2.1.el6
  libasyncns.x86_64 0:0.8-1.1.el6
  libicu.x86_64 0:4.2.1-9.1.el6_2
  libicu-devel.x86_64 0:4.2.1-9.1.el6_2
  libsndfile.x86_64 0:1.0.20-5.el6
  libxcb-devel.x86_64 0:1.9.1-2.el6
  netpbm.x86_64 0:10.47.05-11.el6
  netpbm-progs.x86_64 0:10.47.05-11.el6
  pcre-devel.x86_64 0:7.8-6.el6
  psutils.x86_64 0:1.17-34.el6
  pulseaudio-libs.x86_64 0:0.9.21-17.el6
  rhino.noarch 0:1.7-0.7.r2.2.el6
  tcl-devel.x86_64 1:8.5.7-6.el6
  tex-preview.noarch 0:11.85-10.el6
  texinfo-tex.x86_64 0:4.13a-8.el6
  texlive.x86_64 0:2007-57.el6_2
  texlive-dvips.x86_64 0:2007-57.el6_2
  texlive-latex.x86_64 0:2007-57.el6_2
  texlive-texmf.noarch 0:2007-38.el6
  texlive-texmf-dvips.noarch 0:2007-38.el6
  texlive-texmf-errata.noarch 0:2007-7.1.el6
  texlive-texmf-errata-dvips.noarch 0:2007-7.1.el6
  texlive-texmf-errata-fonts.noarch 0:2007-7.1.el6
  texlive-texmf-errata-latex.noarch 0:2007-7.1.el6
  texlive-texmf-fonts.noarch 0:2007-38.el6
  texlive-texmf-latex.noarch 0:2007-38.el6
  texlive-utils.x86_64 0:2007-57.el6_2
  tk-devel.x86_64 1:8.5.7-5.el6
  ttmkfdir.x86_64 0:3.0.9-32.1.el6
  tzdata-java.noarch 0:2014i-1.el6
  xorg-x11-fonts-Type1.noarch 0:7.2-9.1.el6
  xorg-x11-proto-devel.noarch 0:7.7-9.el6
  xz-devel.x86_64 0:4.999.9-0.5.beta.20091007git.el6

[lewismc]

i installed

Running Transaction
  Installing : php-common-5.3.3-40.el6_6.x86_64                                                  1/3
  Installing : php-pdo-5.3.3-40.el6_6.x86_64                                                     2/3
  Installing : php-mysql-5.3.3-40.el6_6.x86_64                                                   3/3
  Verifying  : php-pdo-5.3.3-40.el6_6.x86_64                                                     1/3
  Verifying  : php-mysql-5.3.3-40.el6_6.x86_64                                                   2/3
  Verifying  : php-common-5.3.3-40.el6_6.x86_64                                                  3/3

Installed:
  php-mysql.x86_64 0:5.3.3-40.el6_6

Dependency Installed:
  php-common.x86_64 0:5.3.3-40.el6_6                 php-pdo.x86_64 0:5.3.3-40.el6_6

Complete!

[lewismc]

I installed

wget rgl_0.95.1157.tar.gz
R CMD install rgl_0.95.1157.tar.gz

[chrismattmann]

OK, please keep commenting on this, but closing this out to mark end of F2F activities quickly approaching.

[cartermp]

I installed:

• Leiningen
• Clojure
• Ring
• Compojure
• Ring-Json

[cartermp]

I installed the iPReS project under the projects folder.

[lewismc]

Thanks @cartermp

[cartermp]

I installed Spyglass, a clojure memcached client. It's currently not working, so it may be uninstalled if I can't get it configured on the system correctly.

[lewismc]

Hi @cartermp please keep us updated, if you cannot install it we can ask politely if @pzimdars can install this on to the box for us. @chrismattmann looping you in on this one as well. Thank you @cartermp

[cartermp]

I'm suspecting the error messaged I'm getting is because memcached isn't installed on the system. It's not listed as a prerequisite for Spyglass, but I think it may be implied because it's a memcached client. I'll play around with this on my local machine before trying to move forward with installing more stuff on here.

(I'm a little green when it comes to sysadminy things, so it may take the weekend)

[cartermp]

I installed:

• clj-http
• core.cache

Into the iPReS folder.

[lewismc]

I'm installing Joshua Decoder under

/usr/local/capstone/joshua-v6.0