removed Summit and added Alpine

docs/software/gaussian.md

@@ -1,18 +1,17 @@
 ## Gaussian
 
-__Important:__ Gaussian is available on Summit only to members of
+__Important:__ Gaussian is available on Alpine only to members of
 universities that have purchased Gaussian licenses. It cannot be run
-by other Summit users. Please note and abide by the licensing,
+by other Alpine users. Please note and abide by the licensing,
 rights, and citation information shown at the top of your Gaussian
 output files.
 
 This document describes how to run G16 jobs efficiently on
-Summit. It does not attempt to teach how to use Gaussian for solving
+Alpine. It does not attempt to teach how to use Gaussian for solving
 science/engineering questions.
 
-Good general instructions can be found at
-[here](http://gaussian.com/running/); however some minor modifications
-are needed when running on Summit.
+Good general instructions can be found [here](http://gaussian.com/running/); however some minor modifications
+are needed when running on Alpine.
 
 
 ### Environment
@@ -24,17 +23,18 @@ not need to source g16.login or g16.profile if running single-node jobs, but if
 
 However, it is important to specify `GAUSS_SCRDIR` to tell G16 where
 to put its large scratch files. These should always be on a [scratch storage system](../compute/filesystems.html)
-(`/scratch/summit/$USER` on Summit or `rc_scratch/$USER` on Blanca.) If `GAUSS_SCRDIR` is not set, then the
+(`/scratch/alpine/$USER` on Alpine or `rc_scratch/$USER` on Blanca.) If 
+`GAUSS_SCRDIR` is not set, then the
 scratch files will be created in whatever directory G16 is run from;
 if this directory is in `/projects` or `/home`, then your job's
 performance will be dramatically reduced.
 
 
 ### Running G16
 
-If you create a Gaussian input file named h2o_dft.com then you can
+If you create a Gaussian input file named `h2o_dft.com` then you can
 execute it simply via `g16 h2o_dft`. Output from the computation will
-go to a file called h2o_dft.log.
+go to a file called `h2o_dft.log`.
 
 
 ### Memory
@@ -66,19 +66,18 @@ __Example SMP BASH script:__
 #!/bin/bash
 
 #SBATCH --job-name=g16-test
-#SBATCH --partition=shas
+#SBATCH --partition=amilan
 #SBATCH --nodes=1
-#SBATCH --ntasks-per-node=24
+#SBATCH --ntasks-per-node=64
 #SBATCH --time=00:50:00
 #SBATCH --output=g16-test.%j.out
 
 module load gaussian/16_avx2
 
 # Always specify a scratch directory on a fast storage space (not /home or /projects!)
-export GAUSS_SCRDIR=/scratch/summit/$USER/$SLURM_JOBID
-# or export GAUSS_SCRDIR=$SLURM_SCRATCH
-# alternatively, to use the local SSD; max 159GB available
-
+export GAUSS_SCRDIR=/scratch/alpine/$USER/$SLURM_JOBID
+# alternatively you can use the local SSD (max 400 GB available)
+# export GAUSS_SCRDIR=$SLURM_SCRATCH
 # the next line prevents OpenMP parallelism from conflicting with Gaussian's internal SMP parallelization
 export OMP_NUM_THREADS=1
 
@@ -91,14 +90,14 @@ date
 
 #### Multi-node (Linda) parallelism
 
-In order to run on more than 24 cores in the "shas" partition on
-Summit, your job will need to span multiple nodes using the Linda
+In order to run on more than 64 cores in the "amilan" partition on
+Alpine, your job will need to span multiple nodes using the Linda
 network parallel communication model. We advise using one Linda worker
 per node, with multiple SMP cores per node. For example, your g16
 flags might include
 
 ```bash
--p=24 -s=ssh -w=shas0521-opa,shas0604-opa,shas0622-opa
+-p=64 -s=ssh -w=c3cpu-a2-u1-2-opa,c3cpu-a2-u1-1-opa,c3cpu-a2-u1-4-opa
 ```
 
 which tells G16 to use 24 cores on each of three shas nodes, and to
@@ -123,10 +122,10 @@ __Linda Parallel__
 #!/bin/bash
 
 #SBATCH --job-name=g16-test
-#SBATCH --partition=shas
+#SBATCH --partition=amilan
 #SBATCH --nodes=2
 #SBATCH --ntasks-per-node=1
-#SBATCH --cpus-per-task=24
+#SBATCH --cpus-per-task=64
 #SBATCH --time=00:50:00
 #SBATCH --output=g16-test.%j.out
 
@@ -138,35 +137,31 @@ for n in `scontrol show hostname | sort -u`; do
 done | paste -s -d, > tsnet.nodes.$SLURM_JOBID
 
 # Always specify a scratch directory on a fast storage space (not /home or /projects!)
-export GAUSS_SCRDIR=/scratch/summit/$USER/$SLURM_JOBID
+export GAUSS_SCRDIR=/scratch/alpine/$USER/$SLURM_JOBID
 
 # the next line prevents OpenMP parallelism from conflicting with Gaussian's internal parallelization
 export OMP_NUM_THREADS=1
 
 # the next line increases the verbosity of Linda output messages
 export GAUSS_LFLAGS="-v"
 
-mkdir $GAUSS_SCRDIR  # only needed if using /scratch/summit
+mkdir $GAUSS_SCRDIR  # only needed if using /scratch/alpine
 date  # put a date stamp in the output file for timing/scaling testing
 g16 -m=20gb -p=24 -w=`cat tsnet.nodes.$SLURM_JOBID` my_input.com
 date
 rm tsnet.nodes.$SLURM_JOBID
 ```
 
 
-#### G16 on GPU
+#### G16 on Alpine NVIDIA GPUs
 
 Please read [http://gaussian.com/running/?tabid=5](http://gaussian.com/running/?tabid=5) carefully to
-determine whether the K80 GPUs in Summit's "sgpu" partition will be
+determine whether the A100 GPUs in Alpine's "aa100" partition will be
 effective for your calculations. In many cases, SMP parallelization
-across all of the cores in a shas node will provide better speedup
+across all of the cores in an amilan node will provide better speedup
 than offloading computational work to a GPU.
 
-
-#### G16 on Knight's Landing
-
-We do not recommend running Gaussian16 on RMACC Summit's "sknl"
-partition.
+G16 can not use the AMD MI100 GPUs in Alpine's "ami100" partition.
 
 ### Sample input file