spaceranger  (spaceranger-1.2.1)
Copyright (c) 2020 10x Genomics, Inc.  All rights reserved.
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Mon Apr 17 16:59:09 EDT 2023

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System Info
uname -a
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Linux cn-0036 3.10.0-1160.31.1.el7.x86_64 #1 SMP Wed May 26 20:18:08 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
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Linux Distro
cat /etc/cm-release /etc/os-release /etc/redhat-release /etc/system-release | sort -u
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ANSI_COLOR="0;31"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
CPE_NAME="cpe:/o:redhat:enterprise_linux:7.9:GA:server"
Cluster Manager v8.1
HOME_URL="https://www.redhat.com/"
ID="rhel"
ID_LIKE="fedora"
NAME="Red Hat Enterprise Linux Server"
PRETTY_NAME="Red Hat Enterprise Linux"
REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.9
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.9"
Red Hat Enterprise Linux Server release 7.9 (Maipo)
VARIANT="Server"
VARIANT_ID="server"
VERSION="7.9 (Maipo)"
VERSION_ID="7.9"
slave
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Kernel Build
cat /proc/version
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Linux version 3.10.0-1160.31.1.el7.x86_64 (mockbuild@x86-040.build.eng.bos.redhat.com) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) ) #1 SMP Wed May 26 20:18:08 UTC 2021
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glibc version
ldd --version | head -n 1
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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 6148 CPU @ 2.40GHz
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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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40
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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 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 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 arat pln pts pku ospke md_clear spec_ctrl intel_stibp
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Memory Total
grep MemTotal /proc/meminfo | cut -d ':' -f 2 | sed 's/^[ \t]*//'
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394896308 kB
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Disk Space
df -Ph | awk '{print $2, $3, $4}'
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Size Used Avail
189G 30M 189G
189G 4.0G 185G
1.2T 14G 1.1T
189G 2.1G 187G
189G 0 189G
1.8T 4.0G 1.7T
969M 747M 156M
100M 0 100M
36G 1016M 33G
36G 352M 34G
89G 201M 84G
178G 413M 168G
89G 64M 84G
18G 45M 17G
14P 12P 2.6P
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Filesystem Options
mount | cut -d ' ' -f 5,6
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proc (rw,nosuid,relatime)
sysfs (rw,relatime)
devtmpfs (rw,relatime,size=197438728k,nr_inodes=49359682,mode=755)
tmpfs (rw,relatime)
ext4 (rw,noatime,nodiratime,data=ordered)
securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs (rw)
devpts (rw,relatime,gid=5,mode=620,ptmxmode=000)
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,freezer)
cgroup (rw,nosuid,nodev,noexec,relatime,net_prio,net_cls)
cgroup (rw,nosuid,nodev,noexec,relatime,blkio)
cgroup (rw,nosuid,nodev,noexec,relatime,devices)
cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)
cgroup (rw,nosuid,nodev,noexec,relatime,cpuacct,cpu)
cgroup (rw,nosuid,nodev,noexec,relatime,memory)
cgroup (rw,nosuid,nodev,noexec,relatime,hugetlb)
cgroup (rw,nosuid,nodev,noexec,relatime,pids)
cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)
autofs (rw,relatime,fd=28,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=699)
mqueue (rw,relatime)
debugfs (rw,relatime)
hugetlbfs (rw,relatime)
configfs (rw,relatime)
binfmt_misc (rw,relatime)
ext4 (rw,noatime,nodiratime,data=ordered)
ext4 (rw,noatime,nodiratime,data=ordered)
vfat (rw,noatime,nodiratime,fmask=0022,dmask=0022,codepage=437,iocharset=ascii,shortname=mixed,errors=remount-ro)
ext4 (rw,noatime,nodiratime,data=ordered)
ext4 (rw,noatime,nodiratime,data=ordered)
ext4 (rw,noatime,nodiratime,data=ordered)
ext4 (rw,noatime,nodiratime,data=ordered)
ext4 (rw,noatime,nodiratime,data=ordered)
ext4 (rw,noatime,nodiratime,data=ordered)
rpc_pipefs (rw,relatime)
gpfs (rw,relatime)
fusectl (rw,relatime)
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User Limits
bash -c 'ulimit -a'
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core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 1542489
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) 134217728
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) 39426457
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited
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User Limits (hard)
bash -c 'ulimit -aH'
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core file size          (blocks, -c) unlimited
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 1542489
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) 134217728
open files                      (-n) 51200
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) 1542489
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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131072
2320	0	131072
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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 = 0
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 = 262144
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 = N
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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22:cpuset:/slurm_cn-0036/uid_1024051431/job_21477321/step_batch
21:pids:/system.slice/slurmd.service
20:hugetlb:/
19:memory:/slurm_cn-0036/uid_1024051431/job_21477321/step_batch
18:cpuacct,cpu:/system.slice/slurmd.service
17:perf_event:/
16:devices:/slurm_cn-0036/uid_1024051431/job_21477321/step_batch/task_0
15:blkio:/system.slice/slurmd.service
14:net_prio,net_cls:/
13:freezer:/slurm_cn-0036/uid_1024051431/job_21477321/step_batch
1:name=systemd:/system.slice/slurmd.service
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cgroup mem stats
cat /sys/fs/cgroup/memory/slurm_cn-0036/uid_1024051431/job_21477321/step_batch/memory.stat
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cache 41558016
rss 3420160
rss_huge 0
mapped_file 1323008
swap 0
pgpgin 35266843
pgpgout 37610550
pgfault 316975422
pgmajfault 1
inactive_anon 0
active_anon 3280896
inactive_file 10526720
active_file 31031296
unevictable 0
hierarchical_memory_limit 137438953472
hierarchical_memsw_limit 137438953472
total_cache 41558016
total_rss 3420160
total_rss_huge 0
total_mapped_file 1323008
total_swap 0
total_pgpgin 0
total_pgpgout 0
total_pgfault 0
total_pgmajfault 0
total_inactive_anon 0
total_active_anon 3280896
total_inactive_file 10526720
total_active_file 31031296
total_unevictable 0
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memory soft limit
cat /sys/fs/cgroup/memory/slurm_cn-0036/uid_1024051431/job_21477321/step_batch/memory.soft_limit_in_bytes
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137438953472
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memory hard limit
cat /sys/fs/cgroup/memory/slurm_cn-0036/uid_1024051431/job_21477321/step_batch/memory.limit_in_bytes
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137438953472
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memory swap limit
cat /sys/fs/cgroup/memory/slurm_cn-0036/uid_1024051431/job_21477321/step_batch/memory.memsw.limit_in_bytes
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137438953472
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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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/cm/shared/apps/slurm/current/bin/qsub
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SGE CLUSTER_NAME
echo $SGE_CLUSTER_NAME
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SGE JOB_NAME
echo $JOB_NAME
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LSF Submit
which bsub
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/cm/shared/apps/slurm/current/bin/bsub
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LSF LSB_JOBNAME
echo $LSB_JOBNAME
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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 "1.8.0_292"
OpenJDK Runtime Environment (build 1.8.0_292-b10)
OpenJDK 64-Bit Server VM (build 25.292-b10, mixed mode)
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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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NODES               MAX_CPUS_PER_NODE   MEMORY              TIMELIMIT           
13                  UNLIMITED           327680+             4:00:00             
73                  UNLIMITED           327680+             12:00:00            
51                  UNLIMITED           327680+             5-00:00:00          
43                  UNLIMITED           327680+             28-00:00:00         
54                  UNLIMITED           327680+             3-00:00:00          
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MRP
mrp --version
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v4.0.2
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mrp templates
ls $(dirname $(dirname $(which mrp)))/jobmanagers/*.template
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