Commit 04a6c9a3 authored by Brandon's avatar Brandon Committed by Kelly L. Rowland

Brandon/https

parent bb20497f
......@@ -76,7 +76,7 @@ Department of Energy guidelines regarding passwords. The following
requirements conform to the Department of Energy guidelines regarding
passwords, namely DOE Order 205.3 and to Lawrence Berkeley National
Laboratory's
[RPM §9.02 Operational Procedures for Computing and Communications](http://www.lbl.gov/Workplace/RPM/R9.02.html).
[RPM §9.02 Operational Procedures for Computing and Communications](https://www.lbl.gov/Workplace/RPM/R9.02.html).
When users are selecting their own passwords for use at NERSC, the
following requirements must be used.
......
......@@ -42,4 +42,4 @@ srun -n 24 epsilon.cplx.x
!!! tip
If after consulting with the above you believe there is an issue
with the NERSC module, please file a
[support ticket](https://help.nersc.gov).
\ No newline at end of file
[support ticket](https://help.nersc.gov).
......@@ -15,7 +15,7 @@ nersc$ module avail cp2k
## Support
* [Reference Manual](https://manual.cp2k.org/)
* [Forum](http://groups.google.com/group/cp2k)
* [Forum](https://groups.google.com/group/cp2k)
* [FAQ](https://www.cp2k.org/faq)
!!! tip
......
......@@ -29,7 +29,7 @@ This script requires that `${INPUT_FILE}` be specified.
## Support
* [User's Guide](http://www.ks.uiuc.edu/Research/namd/current/ug/)
* [Problem with NAMD?](http://www.ks.uiuc.edu/Research/namd/bugreport.html)
* [User's Guide](https://www.ks.uiuc.edu/Research/namd/current/ug/)
* [Problem with NAMD?](https://www.ks.uiuc.edu/Research/namd/bugreport.html)
* **IF** after the above you believe there is an issue with the NERSC
module file a ticket with our [help desk](https://help.nersc.gov)
......@@ -37,4 +37,4 @@ srun -n 24 paratec.mpi
!!! tip
If after consulting with the above you believe there is an issue
with the NERSC module, please file a
[support ticket](https://help.nersc.gov).
\ No newline at end of file
[support ticket](https://help.nersc.gov).
# Quantum ESPRESSO/PWSCF
[Quantum ESPRESSO](http://www.quantum-espresso.org) is an integrated
[Quantum ESPRESSO](https://www.quantum-espresso.org) is an integrated
suite of computer codes for electronic structure calculations and
materials modeling at the nanoscale. It builds on the electronic
structure codes PWscf, PHONON, CP90, FPMD, and Wannier. It is based
......
# Wannier90
The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle
properties and the optical responses of a large variety of materials from bulk periodic
crystals to nanostructures such as slabs, wires and molecules. The package takes as
input the mean-field results from various electronic structure codes such as the
Kohn-Sham DFT eigenvalues and eigenvectors computed with Quantum ESPRESSO, PARATEC,
PARSEC, Octopus, Abinit, Siesta etc.
The BerkeleyGW Package is a set of computer codes that calculates the
quasiparticle properties and the optical responses of a large variety
of materials from bulk periodic crystals to nanostructures such as
slabs, wires and molecules. The package takes as input the mean-field
results from various electronic structure codes such as the Kohn-Sham
DFT eigenvalues and eigenvectors computed with Quantum ESPRESSO,
PARATEC, PARSEC, Octopus, Abinit, Siesta etc.
NERSC provides modules for [Wannier90](https://www.wanier.org).
NERSC provides modules for [Wannier90](http://www.wannier.org).
Use the `module avail` command to see what versions are available:
......@@ -42,4 +43,4 @@ srun -n 24 wannier90.x >& test.log
!!! tip
If after consulting with the above you believe there is an issue
with the NERSC module, please file a
[support ticket](https://help.nersc.gov).
\ No newline at end of file
[support ticket](https://help.nersc.gov).
......@@ -249,7 +249,7 @@ edison
## SSH Control Master
Unlike using [passphraseless ssh with
ssh-agent](http://www.nersc.gov/users/connecting-to-nersc/connecting-with-ssh/),
ssh-agent](https://www.nersc.gov/users/connecting-to-nersc/connecting-with-ssh/),
with MFA, users must enter password + OTP for each ssh connection.
NERSC will be providing tools to allow for single-sign-on type
logins in the near future (see the 'Coming in September, 2018'
......@@ -476,10 +476,10 @@ status of MFA on NERSC systems and services.
[comment]: <> (| Authentication | Host |)
[comment]: <> (|:---:|:---:|)
[comment]: <> (| Shibboleth | Online Help Desk ([https://help.nersc.gov/](https://help.nersc.gov)) |)
[comment]: <> (| | [Science gateways](http://portal.nersc.gov/) with NERSC (Shibboleth) login banner |)
[comment]: <> (| | [Science gateways](https://portal.nersc.gov/) with NERSC (Shibboleth) login banner |)
[comment]: <> (| NEWT | [My NERSC](https://my.nersc.gov/) |)
[comment]: <> (| | [Science gateways](http://portal.nersc.gov/) accepting NIM passwords not displaying the NERSC (Shibboleth) login banner |)
[comment]: <> (| Others | JupyterHubs ([Jupyter](https://ipython.nersc.gov/) and [Jupyter-dev](https://jupyter-dev.nersc.gov/)) |)
[comment]: <> (| | [Science gateways](https://portal.nersc.gov/) accepting NIM passwords not displaying the NERSC (Shibboleth) login banner |)
[comment]: <> (| Others | JupyterHubs ([Jupyter](https://jupyter.nersc.gov/) and [Jupyter-dev](https://jupyter-dev.nersc.gov/)) |)
[comment]: <> (| | [RStudio](https://rstudio.nersc.gov/) |)
[comment]: <> (| | NX and [NX-cloud](https://nxcloud01.nersc.gov/) |)
......@@ -494,24 +494,24 @@ status of MFA on NERSC systems and services.
<td style="text-align: center;">Online Help Desk (<a href="https://help.nersc.gov">https://help.nersc.gov</a>)</td>
</tr>
<tr>
<td style="text-align: center;"><a href="http://portal.nersc.gov/">Science gateways</a> with NERSC (Shibboleth) login banner</td>
<td style="text-align: center;"><a href="https://portal.nersc.gov">Science gateways</a> with NERSC (Shibboleth) login banner</td>
</tr>
<tr>
<td style="text-align: center; vertical-align: middle;" rowspan="2">NEWT</td>
<td style="text-align: center;"><a title="https://my.nersc.gov" href="https://my.nersc.gov">My NERSC</a></td>
</tr>
<tr>
<td style="text-align: center;"><a href="http://portal.nersc.gov/">Science gateways</a> accepting NIM passwords not displaying the&nbsp; NERSC (Shibboleth)&nbsp; login banner</td>
<td style="text-align: center;"><a href="https://portal.nersc.gov">Science gateways</a> accepting NIM passwords not displaying the&nbsp; NERSC (Shibboleth)&nbsp; login banner</td>
</tr>
<tr>
<td style="text-align: center; vertical-align: middle;" rowspan="3">Others</td>
<td style="text-align: center;">JupyterHubs (<a title="https://jupyter.nersc.gov" href="https://ipython.nersc.gov">Jupyter</a>&nbsp;and&nbsp;<a title="https://jupyter-dev.nersc.gov" href="https://jupyter-dev.nersc.gov">Jupyter-dev</a>)</td>
<td style="text-align: center;">JupyterHubs (<a title="https://jupyter.nersc.gov" href="https://jupyter.nersc.gov">Jupyter</a>&nbsp;and&nbsp;<a title="https://jupyter-dev.nersc.gov" href="https://jupyter-dev.nersc.gov">Jupyter-dev</a>)</td>
</tr>
<tr>
<td style="text-align: center;"><a title="https://rstudio.nersc.gov/" href="https://rstudio.nersc.gov/">RStudio</a></td>
<td style="text-align: center;"><a title="https://rstudio.nersc.gov" href="https://rstudio.nersc.gov">RStudio</a></td>
</tr>
<tr>
<td style="text-align: center;">NX and <a title="https://nxcloud01.nersc.gov/" href="https://nxcloud01.nersc.gov/">NX-cloud</a></td>
<td style="text-align: center;">NX and <a title="https://nxcloud01.nersc.gov" href="https://nxcloud01.nersc.gov">NX-cloud</a></td>
</tr>
</tbody>
</table>
......@@ -531,7 +531,7 @@ status of MFA on NERSC systems and services.
</tr>
<tr>
<td style="text-align: center; vertical-align: middle;">-</td>
<td style="text-align: center;"><a title="https://registry.spin.nersc.gov/" href="https://registry.spin.nersc.gov/">NERSC Spin Registry</a></td>
<td style="text-align: center;"><a title="https://registry.spin.nersc.gov" href="https://registry.spin.nersc.gov">NERSC Spin Registry</a></td>
</tr>
</tbody>
</table>
......@@ -540,7 +540,7 @@ status of MFA on NERSC systems and services.
[comment]: <> (| Authentication | Host |)
[comment]: <> (|:---:|:---:|)
[comment]: <> (| - | Other science gateways hosted on [portal.nersc.gov](http://portal.nersc.gov/) |)
[comment]: <> (| - | Other science gateways hosted on [portal.nersc.gov](https://portal.nersc.gov/) |)
[comment]: <> (| | GRDC |)
[comment]: <> (| | WeFold |)
[comment]: <> (| | CRCNS |)
......@@ -555,7 +555,7 @@ status of MFA on NERSC systems and services.
</tr>
<tr>
<td style="text-align: center; vertical-align: middle;" rowspan="6">-</td>
<td style="text-align: center;">Other science gateways hosted on <a href="http://portal.nersc.gov/">portal.nersc.gov</a></td>
<td style="text-align: center;">Other science gateways hosted on <a href="https://portal.nersc.gov/">portal.nersc.gov</a></td>
</tr>
<tr>
<td style="text-align: center;">GRDC</td>
......
......@@ -27,17 +27,17 @@ customize the desktop according to your work requirement.
## Installing
### Download latest NX Client
#### Windows XP/Windows 7/Windows 8 ([Download](http://portal.nersc.gov/project/mpccc/nx/nomachine-enterprise-client_6.0.80_1.exe))
#### Mac OS X 10.5 or later on an Intel Mac ([Download](http://portal.nersc.gov/project/mpccc/nx/nomachine-enterprise-client_6.0.66_2.dmg))
#### DEB Package for Debian/Ubuntu: ([Download](http://portal.nersc.gov/project/mpccc/nx/nomachine-enterprise-client_6.0.66_2_amd64.deb))
#### RPM Package for Centos/Redhat/Fedora ([Download](http://portal.nersc.gov/project/mpccc/nx/nomachine-enterprise-client_6.0.66_2_x86_64.rpm))
#### Windows XP/Windows 7/Windows 8 ([Download](https://portal.nersc.gov/project/mpccc/nx/nomachine-enterprise-client_6.0.80_1.exe))
#### Mac OS X 10.5 or later on an Intel Mac ([Download](https://portal.nersc.gov/project/mpccc/nx/nomachine-enterprise-client_6.0.66_2.dmg))
#### DEB Package for Debian/Ubuntu: ([Download](https://portal.nersc.gov/project/mpccc/nx/nomachine-enterprise-client_6.0.66_2_amd64.deb))
#### RPM Package for Centos/Redhat/Fedora ([Download](https://portal.nersc.gov/project/mpccc/nx/nomachine-enterprise-client_6.0.66_2_x86_64.rpm))
To configure open the NX player and click on the box in the
upper left that says "New". Use "SSH" for protocol,
"nxcloud01.nersc.gov" for host, "password" for authentication,
"Don't use a proxy" for proxy. Alternatively you can [download
the configuration
file](http://portal.nersc.gov/project/mpccc/nx/Connection_to_NERSC_NX_service.nxs.gz)
file](https://portal.nersc.gov/project/mpccc/nx/Connection_to_NERSC_NX_service.nxs.gz)
(you'll need to unzip it and open it with the NX Client).
## Connecting
......@@ -56,7 +56,7 @@ at [nxcloud01](https://nxcloud01.nersc.gov).
If you are having trouble connecting to NX, please can try these steps:
1. Log into [NIM](https://nim.nersc.gov) to clear any login failures. Access to NX uses your NERSC user name and password. If your password is mistyped five times, NERSC will lock you out of their systems. Logging into NIM will automatically clear these failures. This will also let you know if your password is expired (which would prevent you from accessing NX, among many other things).
2. Re-download the [NX configuration file](http://portal.nersc.gov/project/mpccc/nx/Connection_to_NERSC_NX_service.nxs.gz). NX will often "update" the configuration file to try to save your settings and sometimes this file can get some bad settings. You must have the new NX player AND the new configuration file to connect to the NX service.
2. Re-download the [NX configuration file](https://portal.nersc.gov/project/mpccc/nx/Connection_to_NERSC_NX_service.nxs.gz). NX will often "update" the configuration file to try to save your settings and sometimes this file can get some bad settings. You must have the new NX player AND the new configuration file to connect to the NX service.
3. Try to ssh directly to the NX server. You can do this with the command "ssh <nersc_username>@nxcloud01.nersc.gov" and your NERSC user name and password. If your access to the NX server is blocked by a local firewall or something else and you can't connect via ssh, you will also not be able to connect with the NX client.
If you've tried these steps and still cannot connect, please open a help ticket. In this ticket, please include the following information:
......
......@@ -5,7 +5,7 @@ Project Principal Investigators are responsible for meeting OSTP
data management requirements for long-term data sharing and
preservation. The OSTP has issued a memorandum on Increasing Access to
the Results of Federally Funded Scientific Research
(http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf)
(https://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf)
and the DOE has issued a Statement on Digital Data Management.
NERSC resources are intended for users with active allocations, and as
......
......@@ -12,7 +12,7 @@ The output of a datebase join operation is probably better displayed
as two seperate tables.
Example:
[Cori configuration](http://www.nersc.gov/users/computational-systems/cori/configuration/)
[Cori configuration](https://www.nersc.gov/users/computational-systems/cori/configuration/)
| Category | Quantity | Description |
|---------------------|:--------:|--------------------------------------------------------------------------------|
......
......@@ -39,4 +39,4 @@ The module `llvm/5.0.0-gnu-flang` contains `flang` in addition to `clang`. This
##Documentation
For questions about using the Intel compilers at NERSC file a support ticket under [consulting services](https://help.nersc.gov).
For more information, see [LLVM](http://llvm.org/) and [Clang](http://clang.llvm.org/) websites.
\ No newline at end of file
For more information, see [LLVM](https://llvm.org/) and [Clang](https://clang.llvm.org/) websites.
......@@ -151,7 +151,7 @@ The `build_exe` and `install_exe` steps install `python2.7-mpi` which
can easily be relinked to `python-mpi` if the user prefers. The
MPI-enabled Python interpreter is not required
(see
[this page](http://mpi4py.scipy.org/docs/usrman/appendix.html#mpi-enabled-python-interpreter) in
[this page](https://mpi4py.readthedocs.io/en/stable/appendix.html#mpi-enabled-python-interpreter) in
the mpi4py documentation) to use `mpi4py`.
### `h5py` with MPI-IO
......
......@@ -142,4 +142,4 @@ amplxe-cl \
-r ${VTUNE_RESULTS_DIR}
echo -e "\nCompleted\n"
```
\ No newline at end of file
```
......@@ -5,4 +5,4 @@ The Message Passing Interface Standard (MPI) is a message passing library standa
## Resources
* [LLNL Tutorials](https://computing.llnl.gov/tutorials/mpi/)
* [MPI Forum (standards body)](http://mpi-forum.org)
* [MPI Forum (standards body)](https://mpi-forum.org)
......@@ -35,4 +35,4 @@ To use RAJA at NERSC please consult the project's documentation for
the latest information.
* https://github.com/LLNL/RAJA
* [RAJA User Guide](http://raja.readthedocs.io/en/master/)
* [RAJA User Guide](https://raja.readthedocs.io/en/master/)
......@@ -10,7 +10,7 @@ will discuss some examples in more details.
### DESI
[DESI](http://desi.lbl.gov/) jobs use community standard publicly
[DESI](https://desi.lbl.gov/) jobs use community standard publicly
available software, it is independent of the Linux distro flavor. We
show below how to build a Docker image with Ubuntu base.
......@@ -94,7 +94,7 @@ RUN wget https://github.com/GalSim-developers/GalSim/archive/v1.4.2.tar.gz -O Ga
### STAR
The [STAR](http://www.star.bnl.gov/) experiment software stack is
The [STAR](https://www.star.bnl.gov/) experiment software stack is
typically built and run on Scientific Linux.
There are two ways we can build the STAR image, the first is to
......@@ -124,7 +124,7 @@ RUN yum -y install libxml2 tcsh libXpm.i686 libc.i686 libXext.i686 \
wget make libxml2.so.2 gdb libXtst.{i686,x86_64} \
libXt.{i686,x86_64} glibc glibc-devel gcc-c++# Dev Tools
RUN wget -O /etc/yum.repos.d/slc6-devtoolset.repo \
http://linuxsoft.cern.ch/cern/devtoolset/slc6-devtoolset.repo && \
https://linuxsoft.cern.ch/cern/devtoolset/slc6-devtoolset.repo && \
yum -y install devtoolset-2-toolchain
COPY enable_scl /usr/local/star/group/templates/
......@@ -160,7 +160,7 @@ COPY checkProduction.C /usr/local/star//packages/SL16d/StRoot/macros/
# Special RPMs for production at Cori; OpenMpi, mysql-server
RUN yum -y install libibverbs.x86_64 environment-modules infinipath-psm-devel.x86_64 \
librdmacm.x86_64 opensm.x86_64 papi.x86_64 && \
wget http://mirror.centos.org/centos/6.8/os/x86_64/Packages/openmpi-1.10-1.10.2-2.el6.x86_64.rpm && \
wget https://mirror.centos.org/centos/6.8/os/x86_64/Packages/openmpi-1.10-1.10.2-2.el6.x86_64.rpm && \
rpm -i openmpi-1.10-1.10.2-2.el6.x86_64.rpm && \
rm -f openmpi-1.10-1.10.2-2.el6.x86_64.rpm && \
yum -y install glibc-devel devtoolset-2-libstdc++-devel.i686 && \
......
......@@ -105,7 +105,7 @@ RUN cd /build && wget https://www.python.org/ftp/python/2.7.13/Python-2.7.13.tgz
&& tar xvzf Python-2.7.13.tgz && cd /build/Python-2.7.13 \
&& ./configure && make -j4 && make install && make clean && rm /build/Python-2.7.13.tgz
RUN cd /build && wget http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz \
RUN cd /build && wget https://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz \
&& tar xvzf mpich-3.2.tar.gz && cd /build/mpich-3.2 \
&& ./configure && make -j4 && make install && make clean && rm /build/mpich-3.2.tar.gz
......
......@@ -110,7 +110,7 @@ read-only basis. The following command will allow anyone to get a `clone` of
your SG-repository:
```
HTTP_REPO=portal.nersc.gov/project/<project>/git/<git_repository_name>.git
git clone http://${HTTP_REPO} <git_repository_name>
git clone https://${HTTP_REPO} <git_repository_name>
Initialized empty Git repository in .../<git_repository_name>/.git/
```
You now have an L-repository that is a local, read-only clone of the
......@@ -141,7 +141,7 @@ That operation will require authentication via NERSC's LDAP service.
Authenticated access is via the host `portal-auth.nersc.gov`. Your
SG-repository is in the same relative location on `portal-auth` as on `portal`.
```
http://portal-auth.nersc.gov/project/<project>/git/<git_repository_name>.git
https://portal-auth.nersc.gov/project/<project>/git/<git_repository_name>.git
```
The following puts content into a previously empty SG-repository. Updating the
SG-repository with subsequent new content proceeds in the same way. In order to
......@@ -269,7 +269,7 @@ public ones anyway.
You can then access your repositories anonymously via the web at
```
http://portal.nersc.gov/project/<project>/gitweb/gitweb.cgi
https://portal.nersc.gov/project/<project>/gitweb/gitweb.cgi
```
## Troubleshooting
......
......@@ -133,7 +133,7 @@ ln -s /project/projectdirs/<project>/<svn_location> /var/www/svn/<symlink_name>
Once the symlink is setup then checking out a project from the svn repo can be
completed by using the Subversion client:
```
svn co http://portal.nersc.gov/svn/<project>
svn co https://portal.nersc.gov/svn/<project>
```
## Authenticated access to SVN
......
The 1.8 PB NERSC Burst Buffer is based on
Cray [DataWarp](http://www.cray.com/products/storage/datawarp) that
Cray [DataWarp](https://www.cray.com/products/storage/datawarp) that
uses flash or SSD (solid-state drive) technology to significantly
increase the I/O performance on Cori for all file sizes and all access
patterns that sits within the High Speed Network (HSN) on
......
......@@ -4,7 +4,7 @@ Edison has three local scratch file systems named /scratch1,
or the other but not both. The third file system is reserved for users
who need large IO bandwidth, and the access is granted
by
[request](http://www.nersc.gov/users/computational-systems/edison/file-storage-and-i-o/edison-scratch3-directory-request-form/).
[request](https://www.nersc.gov/users/computational-systems/edison/file-storage-and-i-o/edison-scratch3-directory-request-form/).
| Filesystem | Total disk space | Bandwidth |
|------------|:----------------:|:---------:|
......
......@@ -13,7 +13,7 @@ the world.
## Help Desk
The [online help desk](http://help.nersc.gov/) is the **preferred**
The [online help desk](https://help.nersc.gov/) is the **preferred**
method for contacting NERSC.
!!! attention
......@@ -35,7 +35,7 @@ method for contacting NERSC.
### Phone support
The [ticketing system](http://help.nersc.gov/) is the prefered method
The [ticketing system](https://help.nersc.gov/) is the prefered method
of contacting NERSC. NERSC staff can be reached at 1-800-66-NERSC
(USA) or 510-486-8600 (local and international). Consulting and
account support are only available during NERSC business hours (8-5 US
......
......@@ -11,4 +11,4 @@ hero: docs.nersc.gov is in beta
1. [Reset my password](accounts/index.md#forgotten-passwords)
!!!warning "BETA"
Migration of content from [http://www.nersc.gov/users/](http://www.nersc.gov/users/) is underway.
Migration of content from [https://www.nersc.gov/users/](https://www.nersc.gov/users/) is underway.
......@@ -80,7 +80,7 @@ $ root4star -b -q
* Version 5.34/30 23 April 2015 *
* *
* You are welcome to visit our Web site *
* http://root.cern.ch *
* https://root.cern.ch *
* *
*******************************************
......
......@@ -251,7 +251,7 @@ solver.
25-27, 2010. Proceedings, chap. Automatically Tuning Sparse
Matrix-Vector Multiplication for GPU Architectures,
pp. 111–125. Springer Berlin Heidelberg, Berlin, Heidelberg (2010),
http://dx.doi.org/10.1007/978-3-642-11515-8_10
https://dx.doi.org/10.1007/978-3-642-11515-8_10
2. <a name="ref2"></a> Datta, K.: Auto-tuning Stencil Codes for
Cache-Based Multicore Platforms. Ph.D. thesis, EECS Department,
University of California, Berkeley (Dec 2009), http: //www.eecs.b
......@@ -259,7 +259,7 @@ solver.
3. <a name="ref3"></a> Haase, G., Reitzinger, S.: Cache issues of
algebraic multigrid methods for linear systems with multiple
right-hand sides. SIAM Journal on Scientific Computing 27(1), 1–18
(2005), http://dx.doi.org/10.1137/S1064827502405112
(2005), https://dx.doi.org/10.1137/S1064827502405112
4. <a name="ref4"></a> Williams, S.: Auto-tuning Performance on
Multicore Computers. Ph.D. thesis, EECS Department, University of
California, Berkeley (December 2008)
......@@ -269,6 +269,6 @@ solver.
(April 2009)
6. <a name="ref6"></a> Williams, S., Stralen, B.V., Ligocki, T.,
Oliker, L., Cordery, M., Lo, L.: Roofline performance model,
http://crd.lbl.gov/departments/computerscience/PAR/research/roofline/
https://crd.lbl.gov/departments/computerscience/PAR/research/roofline/
7. <a name="ref7"></a> Tal, A.: Intel software development emulator,
https://software.intel.com/en-us/articles/intel-software-development-emulator
......@@ -24,7 +24,7 @@ Modeling of Magnetically Confined Fusion Plasma. The code is version
controlled under git and hosted in bitbucket. For access to the
repository,
please
[contact the main developers](http://epsi.pppl.gov/xgc-users/how-to-become-an-xgc-user).
[contact the main developers](https://epsi.pppl.gov/xgc-users/how-to-become-an-xgc-user).
The XGC1 code has five main kernels:
......@@ -247,4 +247,4 @@ Performance Computing. ISC High Performance 2017. Lecture Notes in Computer
Science, vol 10524. Springer, Cham https://doi.org/10.1007/978-3-319-67630-2_25
[Talk given at NERSC application readiness meeting on 02/14/2018 by T. Koskela
(PDF)](http://www.nersc.gov/assets/Uploads/tkoskela-appReadiness-0214-public.pdf)
(PDF)](https://www.nersc.gov/assets/Uploads/tkoskela-appReadiness-0214-public.pdf)
......@@ -213,4 +213,4 @@ in the **Miscellaneous** tab
Once the project has been created, these settings can be updated via **Settings > Project**.
Here you can download the `CTestConfig.cmake` for the project and also provide a CTest template Script under the **Clients** tab.
![](Images/project_settings.png)
\ No newline at end of file
![](Images/project_settings.png)
......@@ -384,4 +384,4 @@ if __name__ == "__main__":
sys.exit(1)
sys.exit(0)
```
\ No newline at end of file
```
......@@ -192,4 +192,4 @@ Create the following kernel spec (you'll need to make the $SCRATCH/tmpfiles, $SC
"JAVA_HOME":"/usr"
}
}
```
\ No newline at end of file
```
......@@ -107,10 +107,10 @@ consult@nersc.gov.
NERSC Resource | Path On NERSC Resource | URL on the Web
--- | --- | ---
NGF (project filesystem) | /global/project/projectdirs/myproj/www | http://portal.nersc.gov/project/myproj/
NGF (dna filesystem) | /global/dna/projectdirs/myproj/mysubproj/www | http://portal.nersc.gov/dna/myproj/mysubproj/
HPSS archive (home) | /home/m/myuser/www | http://portal.nersc.gov/archive/home/m/myuser/www/
HPSS archive (project) | /home/projects/myproj/www | http://portal.nersc.gov/archive/projects/myproj/www/
NGF (project filesystem) | /global/project/projectdirs/myproj/www | https://portal.nersc.gov/project/myproj/
NGF (dna filesystem) | /global/dna/projectdirs/myproj/mysubproj/www | https://portal.nersc.gov/dna/myproj/mysubproj/
HPSS archive (home) | /home/m/myuser/www | https://portal.nersc.gov/archive/home/m/myuser/www/
HPSS archive (project) | /home/projects/myproj/www | https://portal.nersc.gov/archive/projects/myproj/www/
### Web Methods for Computing
......@@ -159,7 +159,7 @@ the
Science gateways that have moved from development to providing
services to broader communities are listed on
the [Science Gateways index page](http://portal.nersc.gov/).
the [Science Gateways index page](https://portal.nersc.gov/).
Nagios monitoring and service level checks of gateway functions are
available.
......@@ -197,7 +197,7 @@ Copy your data to this www directory. Any public data will need to be
world readable. Add PHP and HTML files to this directory to build
custom gateway interfaces to the data. Any data under
`/global/project/projectdirs/yourproject/www` will be publicly
accessible through `http://portal.nersc.gov/project/yourproject/`.
accessible through `https://portal.nersc.gov/project/yourproject/`.
#### How to publish data in HPSS to the web:
......@@ -213,7 +213,7 @@ infrequent accesses from a data pool that is too large to be
practically kept on the "project" filesystem. If you need to serve
very large files very frequently via a science gateway, please
contact
[NERSC consulting](http://www.nersc.gov/users/getting-help/online-help-desk/) for
[NERSC consulting](https://www.nersc.gov/users/getting-help/online-help-desk/) for
assistance.
Retrieving data from HPSS via a science gateway can be very slow. If
......@@ -242,7 +242,7 @@ the owner of each of them will need to change its permissions:
The data in the www directory will now be available at a URL of the
form
http://portal.nersc.gov/archive/home/projects/DIRNAME/www/{FILE|DIR}
https://portal.nersc.gov/archive/home/projects/DIRNAME/www/{FILE|DIR}
where DIRNAME is the project directory and FILE|DIR is the name of a
file.
......@@ -251,7 +251,7 @@ listing. Note that all files and directories in the path must be world
readable.
Here is an example:
http://portal.nersc.gov/archive/home/projects/incite11/www/1935
https://portal.nersc.gov/archive/home/projects/incite11/www/1935
!!! note
The time to download files from tape may take some time to
......@@ -269,8 +269,8 @@ information, NIM accounting information and object storage.
To get started, insert the following in your HTML files to give you
access to all NERSC compute and data resources through NEWT:
<script src="[http://newt.nersc.gov/js/jquery-1.7.2.js](http://newt.nersc.gov/js/jquery-1.7.2.js)" />
<script src="[http://newt.nersc.gov/js/newt.js](http://newt.nersc.gov/js/newt.js)" />
<script src="[https://newt.nersc.gov/js/jquery-1.7.2.js](https://newt.nersc.gov/js/jquery-1.7.2.js)" />
<script src="[https://newt.nersc.gov/js/newt.js](https://newt.nersc.gov/js/newt.js)" />
Follow the "Hello World" example
at [https://newt.nersc.gov/](https://newt.nersc.gov/), or work through
......
......@@ -235,7 +235,7 @@ can print a large amount of logs, and we removed some here for brevity.
---> 72ef1cf971d1
Step 2/6 : RUN apt-get update --quiet -y && apt-get install --quiet -y python-flask
---> Running in b64e4f148838
Ign:1 http://deb.debian.org/debian stretch InRelease
Ign:1 https://deb.debian.org/debian stretch InRelease
...
...
Removing intermediate container b64e4f148838
......@@ -372,7 +372,7 @@ world.
server {
listen 8080;
location / {
proxy_pass http://app:5000;
proxy_pass https://app:5000;
proxy_set_header Host $host:$server_port;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Host $server_name;
......
......@@ -196,7 +196,7 @@ like we did in lesson 2.
In the following example, I'm inspecting the 'web' container in the
'elvis-flask-demo' stack. From this output, I know my web service is available
at `http://web.elvis-flask-demo.dev-cattle.stable.spin.nersc.org:8080/`. The
at `https://web.elvis-flask-demo.dev-cattle.stable.spin.nersc.org:8080/`. The
web service is also available at an IP address, but note that the IP address may
change from time to time.
......@@ -259,7 +259,7 @@ below. Some steps are not necessary every single time, and may be skipped.
!!! info
For details on the Rancher upgrade commands, see the Rancher documentation at
http://rancher.com/docs/rancher/v1.6/en/cattle/upgrading/ . Note that the
https://rancher.com/docs/rancher/v1.6/en/cattle/upgrading/ . Note that the
Rancher documentation often refers to `rancher-compose`, which is an older
command. Spin uses the `rancher` command instead, which is newer but has most of
the same options. The Rancher documentation mentions 'in-service upgrades' and
......
......@@ -53,4 +53,4 @@ and on the highest likelihood of a successful, working implementation.
Both local and remote participants are welcome.
To see the schedule of the next SpinUp program, please see http://www.nersc.gov/users/data-analytics/spin/
To see the schedule of the next SpinUp program, please see https://www.nersc.gov/users/data-analytics/spin/
......@@ -5,8 +5,8 @@ is available on Cori & Edison to allow NERSC users to manage their
containers, and will soon be available on Denovo.
For more information on using the Rancher CLI, see
[Rancher Command Line Interface (CLI)](http://rancher.com/docs/rancher/v1.6/en/cli/)
on [rancher.com](http://rancher.com).
[Rancher Command Line Interface (CLI)](https://rancher.com/docs/rancher/v1.6/en/cli/)
on [rancher.com](https://rancher.com).
!!! Note
NERSC provides a modified version of the Rancher CLI, and not all commands shown in the Rancher documentation are available to NERSC users.
......@@ -35,7 +35,7 @@ by the following error message:
nersc:test_db $ cat load_dept_emp.dump | rancher exec dbtest/db mysql
ERRO[0012] Failed to handle connection: websocket: bad handshake
error during connect: Get http://%2Fvar%2Ffolders%2Fg8%2Fydzygkc103x9_xt_r8zs6zyr001d77%2FT%2Fdocker-sock578594745/v1.24/exec/6e644e66b9b123123fdf4459a5b23a29f3b079307a664d8b65b68d8d0268169c/json: EOF
error during connect: Get https://%2Fvar%2Ffolders%2Fg8%2Fydzygkc103x9_xt_r8zs6zyr001d77%2FT%2Fdocker-sock578594745/v1.24/exec/6e644e66b9b123123fdf4459a5b23a29f3b079307a664d8b65b68d8d0268169c/json: EOF
nersc:test_db $
### Don't use `rancher run`
......@@ -381,8 +381,8 @@ Logs may be viewed using the `rancher logs` command. The command may use the ser
If your service has more than one container (Remember, a container is an instance of a service), the individual containers logs will show the number of the container at the beginning. In the example below, the 'web' service has two containers. Notice how the line begins with a '01' or a '02' which indicates which container owns that log line.
nersc$ rancher logs elvis-flask-demo/web
01 2018-05-23T00:15:26.486199100Z 128.3.135.223 - - [23/May/2018:00:15:26 +0000] "GET /static/CPvalid1_nodsRNA_40x_Tiles_p1745DAPI.png HTTP/1.1" 200 82055 "http://128.55.206.22:60000/fields/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.181 Safari/537.36" "-"
02 2018-05-23T00:17:21.196355808Z 128.3.135.223 - - [23/May/2018:00:17:21 +0000] "GET /fields/ HTTP/1.1" 200 19322 "http://128.55.206.22:60000/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_4) AppleWebKit/53
01 2018-05-23T00:15:26.486199100Z 128.3.135.223 - - [23/May/2018:00:15:26 +0000] "GET /static/CPvalid1_nodsRNA_40x_Tiles_p1745DAPI.png HTTP/1.1" 200 82055 "https://128.55.206.22:60000/fields/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.181 Safari/537.36" "-"
02 2018-05-23T00:17:21.196355808Z 128.3.135.223 - - [23/May/2018:00:17:21 +0000] "GET /fields/ HTTP/1.1" 200 19322 "https://128.55.206.22:60000/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_4) AppleWebKit/53
nersc$
To view the logs for just a single container, print the container name instead of the service name. The container name can be found using `rancher ps --containers` as shown above.
......
......@@ -140,7 +140,7 @@ Denovo currently supports running images on the login nodes. Cori and Edison do
```bash
denovo> shifter --image=registry.services.nersc.gov/jgi/hmmer:latest hmmscan -h
# hmmscan :: search sequence(s) against a profile database
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# HMMER 3.1b2 (February 2015); https://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
......@@ -158,7 +158,7 @@ denovo> salloc
salloc: Granted job allocation 33066
bash-4.1$ shifter --image=registry.services.nersc.gov/jgi/hmmer:latest hmmscan -h
# hmmscan :: search sequence(s) against a profile database
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# HMMER 3.1b2 (February 2015); https://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
......@@ -189,8 +189,8 @@ NAME="Alpine Linux"
ID=alpine
VERSION_ID=3.5.2
PRETTY_NAME="Alpine Linux v3.5"
HOME_URL="http://alpinelinux.org"
BUG_REPORT_URL="http://bugs.alpinelinux.org"
HOME_URL="https://alpinelinux.org"
BUG_REPORT_URL="https://bugs.alpinelinux.org"
```
So, in this example we specified the image in the #SBATCH directive, and just used `shifter` in the script body to run a command from that container. That's a bit cleaner than having `shifter --image=...` sprinkled throughout the batch script, but we can go one step further. By specifying the image on the `sbatch` submit command, and not in the script, we can make a script that works with several different versions of the container without change. This example simply tells you what OS the container thinks its running, and we can tell the script to run different containers at submit-time:
......@@ -211,8 +211,8 @@ NAME="Alpine Linux"
ID=alpine
VERSION_ID=3.5.2
PRETTY_NAME="Alpine Linux v3.5"
HOME_URL="http://alpinelinux.org"
BUG_REPORT_URL="http://bugs.alpinelinux.org"
HOME_URL="https://alpinelinux.org"
BUG_REPORT_URL="https://bugs.alpinelinux.org"
```
now run the same script with a different image:
......@@ -231,9 +231,9 @@ ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 16.04.2 LTS"
VERSION_ID="16.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
VERSION_CODENAME=xenial
UBUNTU_CODENAME=xenial
```
......
......@@ -30,7 +30,7 @@
<div class="nersc-foot-cell">
<div class="nersc-foot-title">About</div>
<a href="{{ base_url }}/accounts/policy/#acknowledge-use-of-nersc-resources" title="Acknowledge NERSC">Acknowledge NERSC</a><br>
<a href="http://www.nersc.gov/about/contact-us/" title="Contact Us">Contact Us</a><br>
<a href="https://www.nersc.gov/about/contact-us/" title="Contact Us">Contact Us</a><br>
<a href="https://www.lbl.gov/disclaimers/" title="Privacy and Security Notice">Privacy and Security Notice</a><br><br>
<a href="https://science.energy.gov" title="DOE Office of Science">
<img src="{{ base_url }}/img/doe_logo.png">
......
beautifulsoup4==4.6.0
bs4==0.0.1
certifi==2017.11.5
certifi>=2017.11.5
chardet==3.0.4
decorator==4.1.2
idna==2.6
......
......@@ -10,20 +10,23 @@ import argparse
import requests
from bs4 import BeautifulSoup
import validators
import sys
# Known good pages that do not need to be validated. More are appended to this
# list as the script crawls the docs website so that we do not re-validate the
# same pages.
whitelist = ["https://www.lbl.gov/disclaimers/",
whitelist = ["https://www.lbl.gov/disclaimers",
"https://science.energy.gov",
"https://www.lbl.gov",
"https://nxcloud01.nersc.gov",
"http://epsi.pppl.gov/xgc-users/how-to-become-an-xgc-user",
"https://stash.nersc.gov",
"https://stash.nersc.gov:8443",
"http://localhost/",
"https://localhost/",
"http://localhost:5000/",
"https://www.nersc.gov",
"http://localhost",
"https://localhost",
"http://localhost:5000",
"https://localhost:5000",
"https://registry.services.nersc.gov"]
badlist = []
......@@ -52,15 +55,14 @@ def get_url(this_page):
def check_url(page):
"""Function that checks the validity of a URL."""
while True:
url, end_quote = get_url(page)
url_raw, end_quote = get_url(page)
page = page[end_quote:]
if url:
if url_raw:
url = url_raw.rstrip("/")
if not validators.url(url):
print("ERROR: INVALID URL")
try:
if url in whitelist:
print("WHITELIST: {}".format(url))
else:
if url not in whitelist:
print(url)
requests.get(url)
# After a URL has been validated once, add it to the
......@@ -100,7 +102,9 @@ def main():
print("Failed urls:")
for url in badlist:
print(url)
return 1
else:
print("No bad urls!")
return 0
main()
sys.exit(main())
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment