Problem installing yt on NASA Pleiades
Hello, I am a postdoc at Columbia University fairly new to yt and am having trouble installing it on the NASA Pleiades supercomputer. I was hoping that someone else has figured this out before and could help me. I tried running the yt install script obtained with: wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh When I attempt to run this script, it crashes giving the error message copied below. I believe it may be related to the version of ssl on Pleiades. Any help would be greatly appreciated. Thank you! Best, Eli Visbal ----------------------------------------------------------------- ... Installing HDF5 Installing SQLite3 Installing Python 2. This may take a while, but don't worry. yt loves you. Installing setuptools-18.0.1 Installing mercurial-3.4 Cloning yt Setting YT_DIR=/u/evisbal/yt-x86_64/src/yt-hg/ Installing pip ******************************************** FAILURE REPORT: ******************************************** File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/url.py", line 346, in connect **sslutil.sslkwargs(self.ui, host)) File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/sslutil.py", line 36, in ssl_wrap_socket sslcontext.options &= ssl.OP_NO_SSLv2 & ssl.OP_NO_SSLv3 ValueError: can't clear options before OpenSSL 0.9.8m abort: repository /u/evisbal/yt-x86_64/src/yt-hg/ not found! 2015-08-26 14:01:04 URL:https://bootstrap.pypa.io/get-pip.py [1412744/1412744] -> "get-pip.py" [1] Collecting pip Could not find a version that satisfies the requirement pip (from versions: ) No matching distribution found for pip ******************************************** ********************************************
The issue is that the version of openSSL installed on Pleiades is out of date (read insecure), so modern versions of python (specifically, newer than 2.7.9) will refuse to link against it. This breaks pip, among other things. Rather than using the install script, I'd suggest installing yt using miniconda which bundles a build of an up-to-date openSSL: http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda I've been using a setup based on miniconda on Pleiades for the past couple of years with no issue. On Wed, Aug 26, 2015 at 4:44 PM, Eli Visbal <visbal@astro.columbia.edu> wrote:
Hello,
I am a postdoc at Columbia University fairly new to yt and am having trouble installing it on the NASA Pleiades supercomputer. I was hoping that someone else has figured this out before and could help me.
I tried running the yt install script obtained with: wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh
When I attempt to run this script, it crashes giving the error message copied below. I believe it may be related to the version of ssl on Pleiades. Any help would be greatly appreciated. Thank you!
Best, Eli Visbal ----------------------------------------------------------------- ... Installing HDF5 Installing SQLite3 Installing Python 2. This may take a while, but don't worry. yt loves you. Installing setuptools-18.0.1 Installing mercurial-3.4 Cloning yt Setting YT_DIR=/u/evisbal/yt-x86_64/src/yt-hg/ Installing pip ******************************************** FAILURE REPORT: ******************************************** File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/url.py", line 346, in connect **sslutil.sslkwargs(self.ui, host)) File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/sslutil.py", line 36, in ssl_wrap_socket sslcontext.options &= ssl.OP_NO_SSLv2 & ssl.OP_NO_SSLv3 ValueError: can't clear options before OpenSSL 0.9.8m abort: repository /u/evisbal/yt-x86_64/src/yt-hg/ not found! 2015-08-26 14:01:04 URL:https://bootstrap.pypa.io/get-pip.py [1412744/1412744] -> "get-pip.py" [1] Collecting pip Could not find a version that satisfies the requirement pip (from versions: ) No matching distribution found for pip ******************************************** ******************************************** _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Thank you Nathan! That seemed to work. I am having related problems installing Enzo. When I try to obtain the code with "hg clone https://bitbucket.org/enzo/enzo-dev", I find a similar error related to openSSL (error message "ValueError: can't clear options before OpenSSL 0.9.8m"). If you could let me know the easiest alternate way to get Enzo onto Pleiades I would be very grateful. Eli On Wed, Aug 26, 2015 at 6:30 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
The issue is that the version of openSSL installed on Pleiades is out of date (read insecure), so modern versions of python (specifically, newer than 2.7.9) will refuse to link against it. This breaks pip, among other things.
Rather than using the install script, I'd suggest installing yt using miniconda which bundles a build of an up-to-date openSSL:
http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda
I've been using a setup based on miniconda on Pleiades for the past couple of years with no issue.
On Wed, Aug 26, 2015 at 4:44 PM, Eli Visbal <visbal@astro.columbia.edu> wrote:
Hello,
I am a postdoc at Columbia University fairly new to yt and am having trouble installing it on the NASA Pleiades supercomputer. I was hoping that someone else has figured this out before and could help me.
I tried running the yt install script obtained with: wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh
When I attempt to run this script, it crashes giving the error message copied below. I believe it may be related to the version of ssl on Pleiades. Any help would be greatly appreciated. Thank you!
Best, Eli Visbal ----------------------------------------------------------------- ... Installing HDF5 Installing SQLite3 Installing Python 2. This may take a while, but don't worry. yt loves you. Installing setuptools-18.0.1 Installing mercurial-3.4 Cloning yt Setting YT_DIR=/u/evisbal/yt-x86_64/src/yt-hg/ Installing pip ******************************************** FAILURE REPORT: ******************************************** File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/url.py", line 346, in connect **sslutil.sslkwargs(self.ui, host)) File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/sslutil.py", line 36, in ssl_wrap_socket sslcontext.options &= ssl.OP_NO_SSLv2 & ssl.OP_NO_SSLv3 ValueError: can't clear options before OpenSSL 0.9.8m abort: repository /u/evisbal/yt-x86_64/src/yt-hg/ not found! 2015-08-26 14:01:04 URL:https://bootstrap.pypa.io/get-pip.py [1412744/1412744] -> "get-pip.py" [1] Collecting pip Could not find a version that satisfies the requirement pip (from versions: ) No matching distribution found for pip ******************************************** ******************************************** _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
You can install mercurial using conda: "conda install mercurial" That will using conda's SSL library and should fix the issue you're seeing. On Wednesday, August 26, 2015, Eli Visbal <visbal@astro.columbia.edu> wrote:
Thank you Nathan! That seemed to work.
I am having related problems installing Enzo. When I try to obtain the code with "hg clone https://bitbucket.org/enzo/enzo-dev", I find a similar error related to openSSL (error message "ValueError: can't clear options before OpenSSL 0.9.8m"). If you could let me know the easiest alternate way to get Enzo onto Pleiades I would be very grateful.
Eli
The issue is that the version of openSSL installed on Pleiades is out of date (read insecure), so modern versions of python (specifically, newer
2.7.9) will refuse to link against it. This breaks pip, among other
On Wed, Aug 26, 2015 at 6:30 PM, Nathan Goldbaum <nathan12343@gmail.com <javascript:;>> wrote: than things.
Rather than using the install script, I'd suggest installing yt using miniconda which bundles a build of an up-to-date openSSL:
http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda
I've been using a setup based on miniconda on Pleiades for the past
couple
of years with no issue.
On Wed, Aug 26, 2015 at 4:44 PM, Eli Visbal <visbal@astro.columbia.edu <javascript:;>> wrote:
Hello,
I am a postdoc at Columbia University fairly new to yt and am having trouble installing it on the NASA Pleiades supercomputer. I was hoping that someone else has figured this out before and could help me.
I tried running the yt install script obtained with: wget
http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh
When I attempt to run this script, it crashes giving the error message copied below. I believe it may be related to the version of ssl on Pleiades. Any help would be greatly appreciated. Thank you!
Best, Eli Visbal ----------------------------------------------------------------- ... Installing HDF5 Installing SQLite3 Installing Python 2. This may take a while, but don't worry. yt loves
you.
Installing setuptools-18.0.1 Installing mercurial-3.4 Cloning yt Setting YT_DIR=/u/evisbal/yt-x86_64/src/yt-hg/ Installing pip ******************************************** FAILURE REPORT: ******************************************** File "/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/url.py", line 346, in connect **sslutil.sslkwargs(self.ui, host)) File
"/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/sslutil.py",
line 36, in ssl_wrap_socket sslcontext.options &= ssl.OP_NO_SSLv2 & ssl.OP_NO_SSLv3 ValueError: can't clear options before OpenSSL 0.9.8m abort: repository /u/evisbal/yt-x86_64/src/yt-hg/ not found! 2015-08-26 14:01:04 URL:https://bootstrap.pypa.io/get-pip.py [1412744/1412744] -> "get-pip.py" [1] Collecting pip Could not find a version that satisfies the requirement pip (from versions: ) No matching distribution found for pip ******************************************** ******************************************** _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <javascript:;> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <javascript:;> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <javascript:;> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
OK, that worked. Thank you! On Wed, Aug 26, 2015 at 7:34 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
You can install mercurial using conda:
"conda install mercurial"
That will using conda's SSL library and should fix the issue you're seeing.
On Wednesday, August 26, 2015, Eli Visbal <visbal@astro.columbia.edu> wrote:
Thank you Nathan! That seemed to work.
I am having related problems installing Enzo. When I try to obtain the code with "hg clone https://bitbucket.org/enzo/enzo-dev", I find a similar error related to openSSL (error message "ValueError: can't clear options before OpenSSL 0.9.8m"). If you could let me know the easiest alternate way to get Enzo onto Pleiades I would be very grateful.
Eli
On Wed, Aug 26, 2015 at 6:30 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
The issue is that the version of openSSL installed on Pleiades is out of date (read insecure), so modern versions of python (specifically, newer than 2.7.9) will refuse to link against it. This breaks pip, among other things.
Rather than using the install script, I'd suggest installing yt using miniconda which bundles a build of an up-to-date openSSL:
http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda
I've been using a setup based on miniconda on Pleiades for the past couple of years with no issue.
On Wed, Aug 26, 2015 at 4:44 PM, Eli Visbal <visbal@astro.columbia.edu> wrote:
Hello,
I am a postdoc at Columbia University fairly new to yt and am having trouble installing it on the NASA Pleiades supercomputer. I was hoping that someone else has figured this out before and could help me.
I tried running the yt install script obtained with: wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh
When I attempt to run this script, it crashes giving the error message copied below. I believe it may be related to the version of ssl on Pleiades. Any help would be greatly appreciated. Thank you!
Best, Eli Visbal ----------------------------------------------------------------- ... Installing HDF5 Installing SQLite3 Installing Python 2. This may take a while, but don't worry. yt loves you. Installing setuptools-18.0.1 Installing mercurial-3.4 Cloning yt Setting YT_DIR=/u/evisbal/yt-x86_64/src/yt-hg/ Installing pip ******************************************** FAILURE REPORT: ******************************************** File
"/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/url.py", line 346, in connect **sslutil.sslkwargs(self.ui, host)) File
"/home1/evisbal/yt-x86_64/lib/python2.7/site-packages/mercurial/sslutil.py", line 36, in ssl_wrap_socket sslcontext.options &= ssl.OP_NO_SSLv2 & ssl.OP_NO_SSLv3 ValueError: can't clear options before OpenSSL 0.9.8m abort: repository /u/evisbal/yt-x86_64/src/yt-hg/ not found! 2015-08-26 14:01:04 URL:https://bootstrap.pypa.io/get-pip.py [1412744/1412744] -> "get-pip.py" [1] Collecting pip Could not find a version that satisfies the requirement pip (from versions: ) No matching distribution found for pip ******************************************** ******************************************** _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (2)
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Eli Visbal -
Nathan Goldbaum