addressing Guangzhen's comments on PR

Author: haniyeka

docs/userguides/negishi/accounts.md

@@ -25,3 +25,5 @@ search:
 ## Purchasing Nodes
 
 --8<-- "docs/snippets/purchase_nodes.md"
+
+[**Back to Negishi User Guide**](index.md)

docs/userguides/negishi/biography.md

@@ -15,3 +15,5 @@ search:
 Ei-ichi Negishi (1935-2021) was the Herbert C. Brown Distinguished Professor in the Department of Chemistry at Purdue. He came to Purdue in 1966 as a postdoctoral researcher in the lab of the Late Herbert C. Brown, and published 33 papers with Prof. Brown up through the time that Prof. Brown was awarded the Nobel Prize in Chemistry in 1979. With the award of the Nobel to Ei-ichi Negishi in 2010, Purdue has the rare distinction of a pair of Nobel Prize awards in two closely related areas. Professor Negishi’s Nobel Prize was awarded in recognition of his work on palladium-catalyzed cross-coupling chemistry (known world-– wide as the Negishi coupling). That work was described by the Nobel Foundation as "great art in a test tube". This is certainly appropriate as great scientists regard themselves as artists and explorers. The impact of that work was widespread, as it had been used in synthetic organic chemistry research worldwide, as well as in the commercial production of an array of pharmaceuticals and molecules used in the electronics industry. In recognition of and consistent with this idea, Ei-ichi and co-recipient Akira Suzuki were recently awarded Japan's highest cultural award, the "Order of Culture", bestowed in Nov. 2010 by the Emperor.
 
 Professor Negishi was a prolific researcher, with ~400 publications on an array of problems in synthetic organic chemistry, leading to numerous awards. To name just a few, the list includes the Chemical Society of Japan Award (1997), the American Chemical Society Award in Organometallic Chemistry (1998), the McCoy Award (1998), the Sigma Xi Award at Purdue (2003), the Nobel Prize in Chemistry (2010), the Order of Culture in Japan (2010), the American Chemical Society Award for Creative Work in Synthetic Organic Chemistry (2010), the Indiana Sagamore of the Wabash (2011) and the Purdue Order of the Griffin (2011). He was elected to the American Academy of Arts and Sciences in 2011. Professor Negishi was leading the Negishi-Brown Institute, which had continued his work on catalytic organic synthesis. Dr. Negishi was passionate about the prospects for catalytic approaches to the reduction of carbon dioxide to enable large scale production of useful products from this environmental waste product. It is very fitting that Purdue bestow an honorary doctorate degree on Professor Negishi, whose accomplishments and contributions will have a permanent impact on Purdue’s stature and global recognition.
+
+[**Back to Negishi User Guide**](index.md)

docs/userguides/negishi/faqs.md

@@ -29,10 +29,9 @@ Negishi differs from the previous Community Clusters in several significant aspe
 * GCC compiler with OpenMPI or MVAPICH2 MPI libraries are recommended for software development on Negishi. You can enable this software with `module load gcc openmpi` (default) or `module load gcc mvapich2`.
 * If you use Jupyter notebooks, JupyterHub on Negishi will be available only via the [OnDemand Gateway](https://gateway.negishi.rcac.purdue.edu) rather than the freestanding version as on some previous systems. Other RCAC systems will transition to OnDemand as well, following Negishi.
 
-Upcoming 2023
--------------
+#### Upcoming 2023
 
-* A subset of Negishi compute nodes contain ${resource.gpuname} accelerator cards which can significantly improve performance of compute-intensive workloads. These can be utilized by submitting jobs to the `${resource.gpuqueue}` queue (add `-A ${resource.gpuqueue}` to your job submission command).
+* A subset of Negishi compute nodes contain AMD Radeon Instinct MI210 accelerator cards which can significantly improve performance of compute-intensive workloads. These can be utilized by submitting jobs to the `gpu` queue (add `-A gpu` to your job submission command).
 * A selection of GPU-enabled ROCm application containers from the AMD InfinityHub collection is installed.
 
 

docs/userguides/negishi/index.md

@@ -1,8 +1,9 @@
 ---
-#tags:
-#  - Negishi
+tags:
+  - Negishi
 authors:
   - hkashgar
+resource: Negishi
 search:
   boost: 2
 ---
@@ -21,3 +22,4 @@ Negishi is a Community Cluster optimized for communities running traditional, ti
 - [**Compiling Source Code**](compile.md)
 - [**Frequently Asked Questions**](faqs.md)
 
+

docs/userguides/negishi/overview.md

@@ -10,9 +10,9 @@ search:
 
 # Negishi Overview
 
-Negishi is a Community Cluster optimized for communities running traditional, tightly-coupled science and engineering applications. Negishi is being built through a partnership with Dell and AMD over the summer of 2022. Negishi consists of Dell compute nodes with two 64-core AMD Epyc "Milan" processors (128 cores per node) and 256 GB of memory. All nodes have 100 Gbps HDR Infiniband interconnect and a 6-year warranty.
+Negishi is a Community Cluster optimized for communities running traditional, tightly-coupled science and engineering applications. Negishi was built through a partnership with Dell and AMD over the summer of 2022. Negishi consists of Dell compute nodes with two 64-core AMD Epyc "Milan" processors (128 cores per node) and 256 GB of memory. All nodes have 100 Gbps HDR Infiniband interconnect and a 6-year warranty.
 
-New with Negishi is that access is being offered on the basis of each 64-core Rome processor, or a half-node share. To purchase access to Negishi today, go to the [Cluster Access Purchase](https://www.rcac.purdue.edu/purchase) page. Please subscribe to our Community Cluster Program Mailing List to stay informed on the latest purchasing developments or contact us via email at [rcac-cluster-purchase@lists.purdue.edu](mailto:rcac-cluster-purchase@lists.purdue.edu) if you have any questions.
+New with Negishi is that access is being offered on the basis of each 64-core Milan processor, or a half-node share. To purchase access to Negishi today, go to the [Cluster Access Purchase](https://www.rcac.purdue.edu/purchase) page. Please subscribe to our Community Cluster Program Mailing List to stay informed on the latest purchasing developments or contact us via email at [rcac-cluster-purchase@lists.purdue.edu](mailto:rcac-cluster-purchase@lists.purdue.edu) if you have any questions.
 
 ## Negishi Interactive 
 
@@ -49,3 +49,4 @@ On Negishi, the following set of compiler and message-passing libraries for para
 * OpenMPI or MVAPICH2
 
 
+[**Back to Negishi User Guide**](index.md)

docs/userguides/negishi/run_jobs/creating_the_submission_script.md

@@ -8,7 +8,7 @@ search:
   boost: 2
 ---
 
-# Creatting the Slurm Job Submission Script
+# Creating the Slurm Job Submission Script
 
 ### Script
 

docs/userguides/negishi/run_jobs/index.md

@@ -49,3 +49,4 @@ Batch jobs submitted via SLURM have four main steps:
 - [**MPI**](mpi_jobs.md)
 - [**OpenMP**](openmp_jobs.md)
 
+[**Back to Negishi User Guide**](../index.md)

docs/userguides/negishi/run_jobs/interactive_jobs.md

@@ -17,7 +17,7 @@ To submit an interactive job, use ```sinteractive``` to run a login shell on all
 ```sinteractive``` accepts most of the same resource requests as ```sbatch```, so to request a login shell on the cpu account while allocating 2 nodes and 128 total cores, you might do:
 
 ```bash
-sinteractive -A cpu -N2 -n256
+sinteractive -A myaccount -p cpu -N2 -n256
 ```
 
 To quit your interactive job:

docs/userguides/negishi/run_jobs/queues.md

@@ -36,7 +36,7 @@ On Negishi, the various types of nodes on the cluster are organized into distinc
 
 ### CPU Partition
 
-This partition contains the resources a group purchases access to when they purchase CPU resources on Negishi and is made up of 446 Bell-A nodes. Each of these nodes contains two Zen 3 AMD EPYC 7763 64-core processors for a total of 128 cores and 256 GB of memory for a total of more than 57,000 cores in the partition. Memory in this partition is allocated proportional to your core request such that each core is given about 2 GB of memory per core requested. Submission to this partition can be accomplished by using the option: `-p cpu` or `--partition=cpu`.
+This partition contains the resources a group purchases access to when they purchase CPU resources on Negishi and is made up of 450 Negishi-A nodes. Each of these nodes contains two Zen 3 AMD EPYC 7763 64-core processors for a total of 128 cores and 256 GB of memory for a total of more than 57,000 cores in the partition. Memory in this partition is allocated proportional to your core request such that each core is given about 2 GB of memory per core requested. Submission to this partition can be accomplished by using the option: `-p cpu` or `--partition=cpu`.
 
 The purchasing model for this partition allows groups to purchase high priority access to some number of cores. When an account uses resources in this account by submitting a job tagged with the `normal` QOS, the cores used by that job are withdrawn from the account and deposited back into the account when the job terminates.
 
@@ -55,7 +55,7 @@ Available QOSes: `normal`, `standby`
 
 ### Highmem Partition
 
-This partition is made up of 6 Bell-B nodes which have four times as much memory as a standard Bell-A node, and access to this partition is given to all accounts on the cluster to enable work that has higher memory requirements. Each of these nodes contains two Zen 2 AMD EPYC 7763 64-core processors for a total of 128 cores and 1 TB of memory. Memory in this partition is allocated proportional to your core request such that each core is given about 8 GB of memory per core requested. Submission to this partition can be accomplished by using the option: `-p highmem` or `--partition=highmem`.
+This partition is made up of 6 Negishi-B nodes which have four times as much memory as a standard Negishi-A node, and access to this partition is given to all accounts on the cluster to enable work that has higher memory requirements. Each of these nodes contains two Zen 3 AMD EPYC 7763 64-core processors for a total of 128 cores and 1 TB of memory. Memory in this partition is allocated proportional to your core request such that each core is given about 8 GB of memory per core requested. Submission to this partition can be accomplished by using the option: `-p highmem` or `--partition=highmem`.
 
 When using the Highmem partition, jobs are tagged by the `normal` QOS by default, and this is the only QOS that is available for this partition, so there is no need to specify a QOS when using this partition. Additionally jobs are tagged by a highmem partition QOS that enforces the following policies
 
@@ -69,7 +69,7 @@ Available QOSes: `normal`
 
 ### GPU Partition
 
-This partition is made up of 5 Negishi-G nodes. Each of these nodes contains two AMD MI210s and two Zen 2 AMD EPYC 7313 16-core processors for a total of 32 cores and 512GB of memory. Memory in this partition is allocated proportional to your core request such that each core is given about 8 GB of memory per core requested. You should request cores proportional to the number of GPUs you are using in this partition (i.e. if you only need one of the two GPUs, you should request half of the cores on the node) Submission to this partition can be accomplished by using the option: `-p gpu` or `--partition=gpu`.
+This partition is made up of 5 Negishi-G nodes. Each of these nodes contains three AMD MI210s and two Zen 3 AMD EPYC 7313 16-core processors for a total of 32 cores and 512GB of memory. Memory in this partition is allocated proportional to your core request such that each core is given about 16 GB of memory per core requested. You should request cores proportional to the number of GPUs you are using in this partition (i.e. if you only need one of the two GPUs, you should request half of the cores on the node) Submission to this partition can be accomplished by using the option: `-p gpu` or `--partition=gpu`.
 
 When using the gpu partition, jobs are tagged by the `normal` QOS by default, and this is the only QOS that is available for this partition, so there is no need to specify a QOS when using this partition. Additionally jobs are tagged by a gpu partition QOS that enforces the following policies
 
@@ -82,10 +82,10 @@ Available QOSes: `normal`
 
 ### Login Partition
 
-This partition contains the resources a group purchases access to when they purchase "interactive access" on Negishi. Interactive access allows submission of jobs directly to the front ends for immediate job start times. These jobs can only request up to 4 CPUs and 8 GB of memory each and interactive users can only have one job at a time. Submission to this partition can be accomplished by using the option: `-p login` or `--partition=login`. In order to use this partition, you must submit using the interactive QOS which enforces the following policies:
+This partition contains the resources a group purchases access to when they purchase "interactive access" on Negishi. Interactive access allows submission of jobs directly to the front ends for immediate job start times. These jobs can only request up to 4 CPUs and 16 GB of memory each and interactive users can only have one job at a time. Submission to this partition can be accomplished by using the option: `-p login` or `--partition=login`. In order to use this partition, you must submit using the interactive QOS which enforces the following policies:
 
 1. You can have one job running at a time.
-2. You can use up to 4 cores and 8 GB of memory at a time.
+2. You can use up to 4 cores and 16 GB of memory at a time.
 3. Jobs can run for up to 24 hours.
 
 Available QOSes: `interactive`
@@ -118,4 +118,4 @@ In order for a job to use a Job QOS, the user submitting the job must have acces
 Some of these QOSes may not be available in every partition. Each of the partitions in the following section will enumerate which of these QOSes are allowed in the partition.
 
 
-[**Back to the Running Jobs section**](index.md)
+[**Back to the Running Jobs section**](index.md)

docs/userguides/negishi/software.md

@@ -85,4 +85,6 @@ Pre-downloaded bioinformatics containers with module wrappers are available. You
 ```bash
 $ module load biocontainers
 ```
-More information on pre-downloaded ROCm containers can be found [here](https://biocontainer-doc.readthedocs.io/).
+More information on pre-downloaded Biocontainers can be found [here](https://biocontainer-doc.readthedocs.io/).
+
+[**Back to Negishi User Guide**](index.md)