From 4098b5fe4807dc7ccb2c8e3c689dfafa997ee4f0 Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@gmail.com>
Date: Mon, 22 Jul 2019 11:39:12 +0200
Subject: [PATCH] Removing top-level scripts

Scripts will split into several cluster lanes
---
 .cluster_script.sh.swp | Bin 12288 -> 0 bytes
 cluster_info.json      |  11 ---------
 cluster_script.sh      |  52 -----------------------------------------
 3 files changed, 63 deletions(-)
 delete mode 100644 .cluster_script.sh.swp
 delete mode 100644 cluster_info.json
 delete mode 100644 cluster_script.sh

diff --git a/.cluster_script.sh.swp b/.cluster_script.sh.swp
deleted file mode 100644
index 3f14acb5997252df2a7b1d86ad68af76349ae7e7..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 12288
zcmeHNJ!~9B6rKPg;U@t>k%H#s?7~LbyK@o(IC5b-QLq$;$i|@v(J{9>cQ;{oXFW4}
zjxi@hK}7)_6o{IVf(n5UEp&7glr)Hrf(9hM+1>l`<ziAHfo7ynd;8}7%{TAO%JQ_E
zH#auv#rg$?@ib$f{&M_{^S{3T$ac<HJC=Qswv3xPY9vC(G7aLOd9I!rSr2=&wHw{6
zV;T{+yfJj$2=%@)8P{PWRB1<c8)2LqD|E|*T4uIx?&E8A1TXarcm`%NklRl1(n)sy
z+)~rc&(+S*v(N0zRP{p7fM>un;2H1?cm_NJo&nE*XW;+IfX$Avcd@jGs^wj*p2w!1
z)vJGa20R0v0ndPEz%$?(@C<kcJOiEq&wyvZGw>f|fJcn!M;YrJNAmdp|M2hs-=1RZ
z3*ZyrRp2!6^C`yO0|@x`BxAe41>pB58T%550Rnz{g0atm1E2<c^EhK)0UrS$0$ae#
zz-izF@Z)2QeGPmJXy8rY8c+uU;5mQ+f1P0LGhi3E4y*#FfQNxUk^djS55V`pcfbcg
zAIO0&;MOPrKRg4T0ndPEz%%eKF>r7|I!{|+6479QuTa=iR68WBRl@b1%d4%M8`~Re
z*RHfKU%9!ler21MY5ri=#GuA{%Gi`A0#5H{N?V$xw=&QBT*kZ|i&iB1hD9nBj4(Q~
zcuf6tuZJzBJ)E6~9~s>pS&P_|9-XZl)Am#PvO~9SQSdg^rgE#%?b~#TY)_=j`57tB
zFQkYld0-Mrfut$}3WD8S==~s6NtRm?@GLVcnT#;eQ99vvB{coBsp<(H3B5SsK2i)C
zRAxpprTGOTcBx5AFDzbSQwyloaBFINZS}SFSKwLP#YM$PtW<X&ySV!}J!^1#azd7>
zNSKwSu|yCG;ErmyBB@)vZBQ8vyw-)*V<mMTC6(K;Qjmyb<>G~Av$?s(=Eg}nF=8xe
zp0v8{=a-<c_>N31B5kfYZbxJ6E2D0fPde#pqz&0JJf%4tWx1>2QIynW=qAFci2#cU
zTxrtil4lF5nO1j1Xj?gUXfSXR$3gi9hUe(@9=Fs{ajf<XNkg2BOtM(e_O+d@O)4*j
zE<@8P!+h*LH$oQy2LlSmavI51$JJHwjvojUYQe3D3MtZ{h1}#kj`xYDBoegDVim;Y
zSSX`j;Jq3F72*EbZNm2n7hEkzk>R>)D9ohea`8i_?irAiRelk>%HlA0LxV%gl}csc
z4jrz$uC|8Sg?GsEM5NY`Rn!)gabp|}YRuZ6JFzM^drH5BJGpI{wlZ#emA8OUwJJu>
z!5&grJ9bC=L8TcMo+LbtCYX#>w{TRIeVNiMUr@vmg}rxu>YU%p#khOi3h$Fs#R@@r
zB8|hQN0__PfHKNf>HQ(KMN=In*2Q;O@<iomGwk2i>L#T^L?9Pif7P|8i*xkIjZC{G
zmrA>+RNaaWP@5_&D)#D)9aDcGZ^*(3Yn{tk-v%;n+t3RYz1XfukVqp#dG<g7icK%C
zZKFGTBFbZ-sn{^IZ`rTZ<9$(tz;TkP)X27sr7g%jf{g3Risgz4WVI*b*mW-?@Qk9`
zC&vRB%XP89j#h~~&k5brtTt+VXiWwxHwtrYmusi=Q|?rqCM?TS?I_E2mqBS+*^NK-
z_u9FyR4mXkRaYQ)UF^1U{WjbL=V*2K$)-Nn(tW#)JM}Q*I&AyK>el+OF39BVL>eO%
jj+f%%JXwJ_sFb2}ij$MgooVDoH_*imk@l(0ak>6)WSHzu

diff --git a/cluster_info.json b/cluster_info.json
deleted file mode 100644
index 9423084..0000000
--- a/cluster_info.json
+++ /dev/null
@@ -1,11 +0,0 @@
-{
-    "name" : "merlin5",
-    "worker_bin_path" : "/gpfs/data/ozerov_d/cryosparc/cryosparc2_worker/bin/cryosparcw",
-    "cache_path" : "/ssd-scratch/",
-    "send_cmd_tpl" : "{{ command }}",
-    "qsub_cmd_tpl" : "sbatch {{ script_path_abs }}",
-    "qstat_cmd_tpl" : "squeue -j {{ cluster_job_id }}",
-    "qdel_cmd_tpl" : "scancel {{ cluster_job_id }}",
-    "qinfo_cmd_tpl" : "sinfo",
-    "transfer_cmd_tpl" : "cp {{ src_path }} {{ dest_path }}"
-}
diff --git a/cluster_script.sh b/cluster_script.sh
deleted file mode 100644
index 4358cd9..0000000
--- a/cluster_script.sh
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env bash
-#### cryoSPARC cluster submission script template for SLURM
-## Available variables:
-## {{ run_cmd }}            - the complete command string to run the job
-## {{ num_cpu }}            - the number of CPUs needed
-## {{ num_gpu }}            - the number of GPUs needed. 
-##                            Note: the code will use this many GPUs starting from dev id 0
-##                                  the cluster scheduler or this script have the responsibility
-##                                  of setting CUDA_VISIBLE_DEVICES so that the job code ends up
-##                                  using the correct cluster-allocated GPUs.
-## {{ ram_gb }}             - the amount of RAM needed in GB
-## {{ job_dir_abs }}        - absolute path to the job directory
-## {{ project_dir_abs }}    - absolute path to the project dir
-## {{ job_log_path_abs }}   - absolute path to the log file for the job
-## {{ worker_bin_path }}    - absolute path to the cryosparc worker command
-## {{ run_args }}           - arguments to be passed to cryosparcw run
-## {{ project_uid }}        - uid of the project
-## {{ job_uid }}            - uid of the job
-##
-## What follows is a simple SLURM script:
-
-#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }}
-#SBATCH -n {{ num_cpu }}
-##SBATCH --gres=gpu:{{ num_gpu }}
-#SBATCH -p gpu
-##SBATCH --mem={{ (ram_gb*1000)|int }}MB             
-#SBATCH --mem=64000MB
-#SBATCH -o {{ job_dir_abs }}/job.out
-#SBATCH -e {{ job_dir_abs }}/job.err
-#SBATCH --nodes=1
-#SBATCH --exclusive
-#SBATCH --exclude=merlin-g-02
-
-available_devs=""
-for devidx in $(seq 0 15);
-do
-    if [[ -z $(nvidia-smi -i $devidx --query-compute-apps=pid --format=csv,noheader) ]] ; then
-        if [[ -z "$available_devs" ]] ; then
-            available_devs=$devidx
-        else
-            available_devs=$available_devs,$devidx
-        fi
-    fi
-done
-export CUDA_VISIBLE_DEVICES=$available_devs
-
-hostname
-echo "CUDA_VISIBLE_DEVICES : ${CUDA_VISIBLE_DEVICES}"
-echo "{{ run_cmd }}"
-
-{{ run_cmd }}
-