cellranger  (cellranger-7.1.0)
Copyright (c) 2021 10x Genomics, Inc.  All rights reserved.
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Tue Jul  4 13:39:44 MDT 2023

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System Info
uname -a
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Linux dal.lis.ncgr.org 5.14.0-171.el9.x86_64 #1 SMP PREEMPT_DYNAMIC Sat Oct 1 12:56:27 UTC 2022 x86_64 x86_64 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://bugzilla.redhat.com/"
CPE_NAME="cpe:/o:centos:centos:9"
CentOS Stream release 9
HOME_URL="https://centos.org/"
ID="centos"
ID_LIKE="rhel fedora"
LOGO="fedora-logo-icon"
NAME="CentOS Stream"
PLATFORM_ID="platform:el9"
PRETTY_NAME="CentOS Stream 9"
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux 9"
REDHAT_SUPPORT_PRODUCT_VERSION="CentOS Stream"
VERSION="9"
VERSION_ID="9"
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Kernel Build
cat /proc/version
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Linux version 5.14.0-171.el9.x86_64 (mockbuild@x86-05.stream.rdu2.redhat.com) (gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2), GNU ld version 2.35.2-24.el9) #1 SMP PREEMPT_DYNAMIC Sat Oct 1 12:56:27 UTC 2022
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glibc version
ldd --version | head -n 1
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ldd (GNU libc) 2.34
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CPU Model
grep -m 1 'model name' /proc/cpuinfo | cut -d ':' -f 2 | sed 's/^[ \t]*//'
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AMD EPYC 7543 32-Core Processor
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CPU Sockets
grep 'physical id' /proc/cpuinfo | sort -u | wc -l
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2
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CPU Cores
grep -c processor /proc/cpuinfo
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128
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CPU Support
grep -m 1 'flags' /proc/cpuinfo | cut -d ':' -f 2 | sed 's/^\s*//'
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fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf rapl pni pclmulqdq monitor ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 invpcid_single hw_pstate ssbd mba ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 invpcid cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr rdpru wbnoinvd amd_ppin arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload vgif v_spec_ctrl umip pku ospke vaes vpclmulqdq rdpid overflow_recov succor smca
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Memory Total
grep MemTotal /proc/meminfo | cut -d ':' -f 2 | sed 's/^[ \t]*//'
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2113113372 kB
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Disk Space
df -Ph | awk '{print $2, $3, $4}'
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Size Used Avail
4.0M 0 4.0M
1008G 0 1008G
404G 4.1G 399G
1.5T 93G 1.5T
28T 5.6T 23T
1.5G 340M 1.2G
257M 163M 95M
202G 8.0K 202G
262T 66T 197T
441M 441M 0
64M 64M 0
54M 54M 0
202G 12K 202G
54M 54M 0
64M 64M 0
202G 12K 202G
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Filesystem Options
mount | cut -d ' ' -f 5,6
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proc (rw,nosuid,nodev,noexec,relatime)
sysfs (rw,nosuid,nodev,noexec,relatime)
devtmpfs (rw,nosuid,size=4096k,nr_inodes=1048576,mode=755,inode64)
securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs (rw,nosuid,nodev,inode64)
devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs (rw,nosuid,nodev,size=422622676k,nr_inodes=819200,mode=755,inode64)
cgroup2 (rw,nosuid,nodev,noexec,relatime,nsdelegate,memory_recursiveprot)
pstore (rw,nosuid,nodev,noexec,relatime)
efivarfs (rw,nosuid,nodev,noexec,relatime)
bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
xfs (rw,relatime,attr2,inode64,logbufs=8,logbsize=32k,noquota)
autofs (rw,relatime,fd=31,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=80903)
hugetlbfs (rw,relatime,pagesize=2M)
mqueue (rw,nosuid,nodev,noexec,relatime)
tracefs (rw,nosuid,nodev,noexec,relatime)
debugfs (rw,nosuid,nodev,noexec,relatime)
fusectl (rw,nosuid,nodev,noexec,relatime)
configfs (rw,nosuid,nodev,noexec,relatime)
xfs (rw,relatime,attr2,inode64,logbufs=8,logbsize=32k,sunit=1024,swidth=4096,noquota)
xfs (rw,relatime,attr2,inode64,logbufs=8,logbsize=32k,noquota)
vfat (rw,relatime,fmask=0077,dmask=0077,codepage=437,iocharset=ascii,shortname=winnt,errors=remount-ro)
rpc_pipefs (rw,relatime)
tmpfs (rw,nosuid,nodev,relatime,size=211311336k,nr_inodes=52827834,mode=700,uid=1001,gid=1001,inode64)
nfs (rw,relatime,vers=3,rsize=131072,wsize=131072,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=172.20.1.6,mountvers=3,mountport=705,mountproto=udp,local_lock=none,addr=172.20.1.6)
binfmt_misc (rw,nosuid,nodev,noexec,relatime)
squashfs (ro,nodev,relatime,errors=continue,x-gdu.hide)
squashfs (ro,nodev,relatime,errors=continue,x-gdu.hide)
squashfs (ro,nodev,relatime,errors=continue,x-gdu.hide)
tmpfs (rw,nosuid,nodev,relatime,size=211311336k,nr_inodes=52827834,mode=700,uid=1003,gid=1003,inode64)
squashfs (ro,nodev,relatime,errors=continue,x-gdu.hide)
squashfs (ro,nodev,relatime,errors=continue,x-gdu.hide)
tmpfs (rw,nosuid,nodev,relatime,size=211311336k,nr_inodes=52827834,mode=700,uid=1002,gid=1002,inode64)
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User Limits
bash -c 'ulimit -a'
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real-time non-blocking time  (microseconds, -R) unlimited
core file size              (blocks, -c) 0
data seg size               (kbytes, -d) unlimited
scheduling priority                 (-e) 0
file size                   (blocks, -f) unlimited
pending signals                     (-i) 8254177
max locked memory           (kbytes, -l) 8192
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) 8254177
virtual memory              (kbytes, -v) unlimited
file locks                          (-x) unlimited
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User Limits (hard)
bash -c 'ulimit -aH'
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real-time non-blocking time  (microseconds, -R) unlimited
core file size              (blocks, -c) unlimited
data seg size               (kbytes, -d) unlimited
scheduling priority                 (-e) 0
file size                   (blocks, -f) unlimited
pending signals                     (-i) 8254177
max locked memory           (kbytes, -l) 8192
max memory size             (kbytes, -m) unlimited
open files                          (-n) 524288
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) 8254177
virtual memory              (kbytes, -v) unlimited
file locks                          (-x) unlimited
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Global File Limit
cat /proc/sys/fs/file-{max,nr}
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9223372036854775807
4640	0	9223372036854775807
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Memory config
sysctl vm
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vm.admin_reserve_kbytes = 8192
vm.compact_unevictable_allowed = 1
vm.compaction_proactiveness = 20
vm.dirty_background_bytes = 0
vm.dirty_background_ratio = 10
vm.dirty_bytes = 0
vm.dirty_expire_centisecs = 3000
vm.dirty_ratio = 40
vm.dirty_writeback_centisecs = 500
vm.dirtytime_expire_seconds = 43200
vm.extfrag_threshold = 500
vm.hugetlb_shm_group = 0
vm.laptop_mode = 0
vm.legacy_va_layout = 0
vm.lowmem_reserve_ratio = 256	256	32	0	0
vm.max_map_count = 65530
vm.memory_failure_early_kill = 0
vm.memory_failure_recovery = 1
vm.min_free_kbytes = 405504
vm.min_slab_ratio = 5
vm.min_unmapped_ratio = 1
vm.mmap_min_addr = 65536
vm.nr_hugepages = 0
vm.nr_hugepages_mempolicy = 0
vm.nr_overcommit_hugepages = 0
vm.numa_stat = 1
vm.numa_zonelist_order = Node
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.page_lock_unfairness = 5
vm.panic_on_oom = 0
vm.percpu_pagelist_high_fraction = 0
vm.stat_interval = 1
vm.swappiness = 10
vm.unprivileged_userfaultfd = 0
vm.user_reserve_kbytes = 131072
vm.vfs_cache_pressure = 100
vm.watermark_boost_factor = 15000
vm.watermark_scale_factor = 10
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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0::/user.slice/user-1001.slice/session-903.scope
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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
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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
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Java
which java
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/usr/bin/java
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Java Version
java -version 2>&1 | cat
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openjdk version "11.0.18" 2023-01-17 LTS
OpenJDK Runtime Environment (Red_Hat-11.0.18.0.10-3.el9) (build 11.0.18+10-LTS)
OpenJDK 64-Bit Server VM (Red_Hat-11.0.18.0.10-3.el9) (build 11.0.18+10-LTS, 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
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MRP
mrp --version
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v4.0.10
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mrp templates
ls $(dirname $(dirname $(which mrp)))/jobmanagers/*.template
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