Month: May 2020

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The discovery machines – how supercomputers will shape the future of data-driven science

Research infrastructures play a key role in delivering high quality scientific data to many scientific communities. In the future, we will face a tremendous increase in data volume and rate at these facilities. This will fundamentally change the role of computing at these facilities. With this change new possibilities of using supercomputers for science arise. We will discuss how that future might look like, what is necessary to bring it to reality and – most importantly – how this will allow to foster interdisciplinary science in a complex world.

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Upgrading firmware for Super-Dome Flex

Step 1: Log into the HPE Superdome Flex Server operating system as the root user, and enter the following command to stop the operating system:

# shutdown

 

Step 2: Login to the RMC as administrator user, provide the password when prompted.

Use of DNS is recommended. If using DNS, verify that the RMC is configured to use DNS access by running:

RMC cli> show dns

If not, you may use the command “add dns” to configure DNS access (or you can’t use DNS).

 

Step 3: Enter the following command to power off the system:

If there is only 1 partition, partition 0 is the default:

RMC cli> power off npar pnum=0

In case of multiple partitions, enter show npar to find the partition number, then enter:

RMC cli> power off npar pnum=x

(where x is the partition number)

 

Step 4: Update the firmware by running the command:

RMC cli> update firmware url=<path_to_firmware>

Where <path_to_firmware>  specifies the location to the firmware file that you previously downloaded. You can use https, sftp or scp with an optional port. For instance:

RMC cli> update firmware url=scp://username@myhost.com/sd-flex-<version>-fw.tars
RMC cli> update firmware url=sftp://username@myhost.com/sd-flex-<version>-fw.tars
RMC cli> update firmware url=https://myhost.com/sd-flex-<version>-fw.tars
RMC cli> update firmware url=https://myhost.com:123/sd-flex-<version>-fw.tars

Note: The CLI does not accept clear text password, the password has to be manually typed in.

Note: To use a hostname like ‘myhost.com’, RMC must be configured for DNS for name resolution, otherwise you need to specify the IP address of ‘myhost.com’ instead. See the command ‘add dns’ for more information.

 

Step 5: Wait for RMC to reboot after a successful FW update, then check the new firmware version installed by running:

RMC cli> show firmware verbose

Note: The nPar firmware version will not be updated until the next nPar reboot. See output under “DETERMINING CURRENT VERSION” below.

 

Step 6: Power on the system or partition:

– To power up a system configured with all chassis in one large nPartition numbered 0, enter:

RMC cli>  power on pnum=0

.- If you have multiple npars, each npar can be powered on separately using:

RMC cli>  power on npar pnum=x

, where x is the partition number.

 

Step 7: Determining Current Version:

To check or verify the current firmware levels on the system, from the CLI, enter the RMC command:

RMC cli>  show firmware

 

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Setting up NBO-7 with Gaussian-16

Taken from NBO-7 README and INSTALL.g16a03 files

Step 1: Unpack the distribution using tar, e.g.,

cp nbo7.0-bin-linux-x64.tar.gz /usr/local
cd /usr/local
tar -zxvf nbo7.0-bin-linux-x64.tar.gz

Step 2: Edit the gaunbo6 script in nbo7/bin.

Set the variables GAUNBO, BINDIR, and INT for your environment. For example, if NBO7 is installed in /usr/local and G16 uses 64-bit integers, set

setenv GAUNBO g16nbo
setenv BINDIR /opt/nbo7/bin
setenv INT i8

cd /usr/local/nbo7/bin
vim gaunbo6
#!/bin/tcsh -f

# See nbo7/tests/gaussian/a03/ALERT for G16 A.03 limitations.

# Use this script (gaunbo6) to perform NBO7 analysis with G09 and
# pre-C.01 revisions of G16. Use the gaunbo7 script with G16 C.01
# and later revisions.

# The directory containing this script should be present in the
# user's path during the Gaussian calculation. Alternatively, simply
# copying this file to $g09root/g09 or $g16root/g16, and editing it
# as described below generally works well.

# Inspect and set, as appropriate, the following three environment
# variables.

# Specify Gaussian interface (g09nbo or g16nbo):

setenv GAUNBO g16nbo

# Specify executable directory:

setenv BINDIR /usr/local/nbo7/bin

# Set integer presentation (i8 or i4, likely the former):

setenv INT i8

.....
.....
.....

Step 3: Ensure that the path to gaunbo6 is included in the path environment variable in your .bashrc

export PATH=$PATH:/usr/local/nbo7/bin

Note
NBO7 tests integer communications to ensure that G16 and NBO7 are using the same integer lengths. If NBO7 fails, try switching the integer length (i.e. from i8 or i4, or vice versa).

Users request NBO7 analysis using Gaussian keywords of the following forms:

pop=nbo6 — default NBO7 analysis, no $NBO input
pop=nbo6read — NBO7 analysis with $NBO input
pop=nbo6del — NBO7 analysis with deletions
pop=(nbo6,savenbos) — default NBO7 analysis, save NBOs, sorted by energy, on the checkpoint file
pop=(nbo6,savenlmos) — default NBO7 analysis, save NLMOs on the checkpoint file

Note that these keywords are analogous to the pop=nbo, pop=nboread, etc. keywords that are used to run the old NBO 3.1 analysis (Link 607) of G16.