cellranger-arc  (cellranger-arc-2.0.2)
Copyright (c) 2021 10x Genomics, Inc.  All rights reserved.
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Tue Dec  5 01:57:07 EST 2023

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System Info
uname -a
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Linux b8.private 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 x86_64 GNU/Linux
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Linux Distro
cat /etc/*-release | sort -u
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ANSI_COLOR="0;31"
BUG_REPORT_URL="https://bugs.centos.org/"
CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
CPE_NAME="cpe:/o:centos:centos:7"
CentOS Linux release 7.8.2003 (Core)
HOME_URL="https://www.centos.org/"
ID="centos"
ID_LIKE="rhel fedora"
NAME="CentOS Linux"
PRETTY_NAME="CentOS Linux 7 (Core)"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"
VERSION="7 (Core)"
VERSION_ID="7"
=====================================================================

=====================================================================
Kernel Build
cat /proc/version
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Linux version 3.10.0-1127.19.1.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-39) (GCC) ) #1 SMP Tue Aug 25 17:23:54 UTC 2020
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=====================================================================
glibc version
ldd --version | head -n 1
---------------------------------------------------------------------
ldd (GNU libc) 2.17
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CPU Model
grep -m 1 'model name' /proc/cpuinfo | cut -d ':' -f 2 | sed 's/^[ \t]*//'
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Intel(R) Xeon(R) Gold 5220R CPU @ 2.20GHz
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CPU Sockets
grep 'physical id' /proc/cpuinfo | sort -u | wc -l
---------------------------------------------------------------------
2
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CPU Cores
grep -c processor /proc/cpuinfo
---------------------------------------------------------------------
96
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CPU Support
grep -m 1 'flags' /proc/cpuinfo | cut -d ':' -f 2 | sed 's/^\s*//'
---------------------------------------------------------------------
fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single intel_ppin intel_pt ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke avx512_vnni md_clear spec_ctrl intel_stibp flush_l1d arch_capabilities
=====================================================================

=====================================================================
Memory Total
grep MemTotal /proc/meminfo | cut -d ':' -f 2 | sed 's/^[ \t]*//'
---------------------------------------------------------------------
394846664 kB
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=====================================================================
Disk Space
df -Ph | awk '{print $2, $3, $4}'
---------------------------------------------------------------------
Size Used Avail
189G 2.1G 187G
189G 45G 144G
189G 0 189G
189G 2.5G 186G
189G 0 189G
413G 152G 241G
2.0T 1.9T 52G
200G 60G 141G
344T 342T 2.3T
474T 464T 11T
38G 0 38G
370T 349T 22T
38G 0 38G
474T 184T 291T
474T 184T 291T
=====================================================================

=====================================================================
Filesystem Options
mount | cut -d ' ' -f 5,6
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tmpfs (rw,relatime)
proc (rw,relatime)
tmpfs (rw,relatime)
sysfs (rw,relatime)
devtmpfs (rw,nosuid,size=197408912k,nr_inodes=49352228,mode=755)
securityfs (rw,nosuid,nodev,noexec,relatime)
selinuxfs (rw,relatime)
tmpfs (rw)
devpts (rw,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs (rw,nosuid,nodev,mode=755)
tmpfs (ro,nosuid,nodev,noexec,mode=755)
cgroup (rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/usr/lib/systemd/systemd-cgroups-agent,name=systemd)
pstore (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime,cpuacct,cpu)
cgroup (rw,nosuid,nodev,noexec,relatime,pids)
cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)
cgroup (rw,nosuid,nodev,noexec,relatime,net_prio,net_cls)
cgroup (rw,nosuid,nodev,noexec,relatime,blkio)
cgroup (rw,nosuid,nodev,noexec,relatime,hugetlb)
cgroup (rw,nosuid,nodev,noexec,relatime,memory)
cgroup (rw,nosuid,nodev,noexec,relatime,freezer)
cgroup (rw,nosuid,nodev,noexec,relatime,devices)
cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)
mqueue (rw,relatime)
hugetlbfs (rw,relatime)
autofs (rw,relatime,fd=31,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=78952)
debugfs (rw,relatime)
configfs (rw,relatime)
ext4 (rw,relatime,data=ordered)
rpc_pipefs (rw,relatime)
nfs (rw,relatime,vers=3,rsize=1024,wsize=1024,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=192.168.2.30,mountvers=3,mountport=20048,mountproto=udp,local_lock=none,addr=192.168.2.30)
nfs (rw,relatime,vers=3,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=192.168.2.30,mountvers=3,mountport=20048,mountproto=udp,local_lock=none,addr=192.168.2.30)
autofs (rw,relatime,fd=5,pgrp=8394,timeout=300,minproto=5,maxproto=5,indirect,pipe_ino=152750)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,indirect,pipe_ino=58461)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
nfs4 (rw,nosuid,nodev,relatime,vers=4.1,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,clientaddr=192.168.2.108,local_lock=none,addr=192.168.2.180)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
nfs4 (rw,nosuid,nodev,relatime,vers=4.1,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,clientaddr=192.168.2.108,local_lock=none,addr=192.168.2.178)
tmpfs (rw,nosuid,nodev,relatime,size=39484668k,mode=700,uid=141872,gid=204879)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
nfs4 (rw,nosuid,nodev,relatime,vers=4.1,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,clientaddr=192.168.2.108,local_lock=none,addr=192.168.2.174)
tmpfs (rw,nosuid,nodev,relatime,size=39484668k,mode=700,uid=182138,gid=204879)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
nfs4 (rw,nosuid,nodev,relatime,vers=4.1,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,clientaddr=192.168.2.108,local_lock=none,addr=192.168.2.177)
autofs (rw,relatime,fd=11,pgrp=8394,timeout=300,minproto=5,maxproto=5,offset,pipe_ino=58461)
nfs4 (rw,nosuid,nodev,relatime,vers=4.1,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,clientaddr=192.168.2.108,local_lock=none,addr=192.168.2.177)
=====================================================================

=====================================================================
User Limits
bash -c 'ulimit -a'
---------------------------------------------------------------------
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 1542257
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited
=====================================================================

=====================================================================
User Limits (hard)
bash -c 'ulimit -aH'
---------------------------------------------------------------------
core file size          (blocks, -c) unlimited
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 1542257
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 4096
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) unlimited
max user processes              (-u) 1542257
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited
=====================================================================

=====================================================================
Global File Limit
cat /proc/sys/fs/file-{max,nr}
---------------------------------------------------------------------
39114648
9024	0	39114648
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Memory config
sysctl vm
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vm.admin_reserve_kbytes = 8192
vm.block_dump = 0
vm.dirty_background_bytes = 0
vm.dirty_background_ratio = 10
vm.dirty_bytes = 0
vm.dirty_expire_centisecs = 3000
vm.dirty_ratio = 20
vm.dirty_writeback_centisecs = 500
vm.drop_caches = 3
vm.extfrag_threshold = 500
vm.hugepages_treat_as_movable = 0
vm.hugetlb_shm_group = 0
vm.laptop_mode = 0
vm.legacy_va_layout = 0
vm.lowmem_reserve_ratio = 256	256	32
vm.max_map_count = 65530
vm.memory_failure_early_kill = 0
vm.memory_failure_recovery = 1
vm.min_free_kbytes = 90112
vm.min_slab_ratio = 5
vm.min_unmapped_ratio = 1
vm.mmap_min_addr = 4096
vm.nr_hugepages = 0
vm.nr_hugepages_mempolicy = 0
vm.nr_overcommit_hugepages = 0
vm.nr_pdflush_threads = 0
vm.numa_zonelist_order = default
vm.oom_dump_tasks = 1
vm.oom_kill_allocating_task = 0
vm.overcommit_kbytes = 0
vm.overcommit_memory = 0
vm.overcommit_ratio = 50
vm.page-cluster = 3
vm.panic_on_oom = 0
vm.percpu_pagelist_fraction = 0
vm.stat_interval = 1
vm.swappiness = 60
vm.user_reserve_kbytes = 131072
vm.vfs_cache_pressure = 100
vm.zone_reclaim_mode = 0
=====================================================================

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THP memory config
cat /sys/kernel/mm/*transparent_hugepage/enabled
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[always] madvise never
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cgroups
cat /proc/self/cgroup
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11:perf_event:/
10:devices:/
9:freezer:/
8:memory:/
7:hugetlb:/
6:blkio:/
5:net_prio,net_cls:/
4:cpuset:/
3:pids:/
2:cpuacct,cpu:/
1:name=systemd:/user.slice/user-182138.slice/session-190623.scope
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cgroup mem stats
cat /sys/fs/cgroup/memory//memory.stat
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cache 59612958720
rss 220454187008
rss_huge 2682257408
mapped_file 33296384
swap 327740407808
pgpgin 2355104240306
pgpgout 2364366816004
pgfault 4141595858966
pgmajfault 6214041598
inactive_anon 11490447360
active_anon 209272541184
inactive_file 12565913600
active_file 46986002432
unevictable 0
hierarchical_memory_limit 9223372036854771712
hierarchical_memsw_limit 9223372036854771712
total_cache 59612958720
total_rss 220454219776
total_rss_huge 2682257408
total_mapped_file 33296384
total_swap 327740407808
total_pgpgin 2355104240314
total_pgpgout 2364366816004
total_pgfault 4141595858982
total_pgmajfault 6214041598
total_inactive_anon 11490447360
total_active_anon 209272541184
total_inactive_file 12565913600
total_active_file 46986002432
total_unevictable 0
=====================================================================

=====================================================================
memory soft limit
cat /sys/fs/cgroup/memory//memory.*soft_limit_in_bytes
---------------------------------------------------------------------
9223372036854771712
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memory hard limit
cat /sys/fs/cgroup/memory//memory.limit_in_bytes
---------------------------------------------------------------------
9223372036854771712
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memory swap limit
cat /sys/fs/cgroup/memory//memory.memsw.limit_in_bytes
---------------------------------------------------------------------
9223372036854771712
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Container
[ -e /.dockerenv ] || [ -e /.dockerinit ] || [ ! -z "$container" ] || grep -m 1 -E 'docker|lxc' /proc/1/cgroup > /dev/null && echo 'Detected'
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init process
head -n 1 /proc/1/sched | cut -d ' ' -f 1
---------------------------------------------------------------------
systemd
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SGE Submit
which qsub
---------------------------------------------------------------------
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LSF Submit
which bsub
---------------------------------------------------------------------
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BCL2FASTQ 1
which configureBclToFastq.pl
---------------------------------------------------------------------
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=====================================================================
BCL2FASTQ 2
which bcl2fastq
---------------------------------------------------------------------
/home/benjames/bin/bcl2fastq
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=====================================================================
BCL2FASTQ 2 Version
bcl2fastq --version
---------------------------------------------------------------------
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Java
which java
---------------------------------------------------------------------
/net/bmc-lab5/data/kellis/group/Benjamin/software/miniconda3/envs/scorch/bin/java
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=====================================================================
Java Version
java -version 2>&1 | cat
---------------------------------------------------------------------
openjdk version "20-internal" 2023-03-21
OpenJDK Runtime Environment (build 20-internal-adhoc..src)
OpenJDK 64-Bit Server VM (build 20-internal-adhoc..src, mixed mode, sharing)
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=====================================================================
10X Refdata
echo $TENX_REFDATA
---------------------------------------------------------------------

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=====================================================================
10X Refdata Version
cat $TENX_REFDATA/version
---------------------------------------------------------------------
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qconf
which qconf
---------------------------------------------------------------------
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=====================================================================
slurm info
sinfo -O nodes,maxcpuspernode,memory,time
---------------------------------------------------------------------
NODES               MAX_CPUS_PER_NODE   MEMORY              TIMELIMIT           
44                  UNLIMITED           95296+              14-00:00:00         
12                  UNLIMITED           384000+             28-00:00:00         
=====================================================================

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MRP
mrp --version
---------------------------------------------------------------------
v4.0.5
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mrp templates
ls $(dirname $(dirname $(which mrp)))/jobmanagers/*.template
---------------------------------------------------------------------
=====================================================================

