cellranger-arc  (cellranger-arc-2.0.0)
Copyright (c) 2021 10x Genomics, Inc.  All rights reserved.
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Fri Aug  6 23:19:19 EDT 2021

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System Info
uname -a
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Linux cn-0008 3.10.0-693.17.1.el7.x86_64 #1 SMP Sun Jan 14 10:36:03 EST 2018 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:redhat:enterprise_linux:7.4: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=7.4
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.4"
Red Hat Enterprise Linux Server release 7.4 (Maipo)
VARIANT="Server"
VARIANT_ID="server"
VERSION="7.4 (Maipo)"
VERSION_ID="7.4"
slave
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Kernel Build
cat /proc/version
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Linux version 3.10.0-693.17.1.el7.x86_64 (mockbuild@x86-041.build.eng.bos.redhat.com) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-16) (GCC) ) #1 SMP Sun Jan 14 10:36:03 EST 2018
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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 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_pt spec_ctrl ibpb_support 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
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Memory Total
grep MemTotal /proc/meminfo | cut -d ':' -f 2 | sed 's/^[ \t]*//'
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394875152 kB
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Disk Space
df -Ph | awk '{print $2, $3, $4}'
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Size Used Avail
1.2T 13G 1.1T
189G 0 189G
189G 2.2G 187G
189G 156K 189G
189G 0 189G
1.8T 2.1G 1.7T
89G 64M 84G
969M 632M 272M
36G 1.3G 33G
89G 444M 84G
36G 208M 34G
178G 229M 168G
100M 0 100M
18G 45M 17G
14P 9.8P 4.1P
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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=197426972k,nr_inodes=49356743,mode=755)
tmpfs (rw,relatime)
ext4 (rw,noatime,nodiratime,data=ordered)
securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs (rw,relatime)
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,cpuacct,cpu)
cgroup (rw,nosuid,nodev,noexec,relatime,memory)
cgroup (rw,nosuid,nodev,noexec,relatime,devices)
cgroup (rw,nosuid,nodev,noexec,relatime,blkio)
cgroup (rw,nosuid,nodev,noexec,relatime,hugetlb)
cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)
cgroup (rw,nosuid,nodev,noexec,relatime,pids)
cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)
autofs (rw,relatime,fd=23,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=44715)
mqueue (rw,relatime)
debugfs (rw,relatime)
hugetlbfs (rw,relatime)
configfs (rw,relatime)
binfmt_misc (rw,relatime)
nfsd (rw,relatime)
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)
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)
rpc_pipefs (rw,relatime)
gpfs (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) 1542398
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) 134217728
open files                      (-n) 65536
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) 1542398
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) 134217728
open files                      (-n) 200000
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) 1542398
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
3200	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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21:cpuset:/slurm_cn-0008/uid_1023655044/job_14004931/step_batch
20:pids:/
19:perf_event:/
18:hugetlb:/
17:blkio:/
16:devices:/slurm_cn-0008/uid_1023655044/job_14004931/step_batch
15:memory:/slurm_cn-0008/uid_1023655044/job_14004931/step_batch
14:cpuacct,cpu:/
13:net_prio,net_cls:/
12:freezer:/slurm_cn-0008/uid_1023655044/job_14004931/step_batch
1:name=systemd:/system.slice/slurmd.service
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cgroup mem stats
cat /sys/fs/cgroup/memory/slurm_cn-0008/uid_1023655044/job_14004931/step_batch/memory.stat
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cache 155303936
rss 3436544
rss_huge 0
mapped_file 1343488
swap 0
pgpgin 258291419
pgpgout 299744842
pgfault 1030777333
pgmajfault 0
inactive_anon 0
active_anon 3334144
inactive_file 115085312
active_file 40202240
unevictable 0
hierarchical_memory_limit 137438953472
hierarchical_memsw_limit 137438953472
total_cache 155303936
total_rss 3436544
total_rss_huge 0
total_mapped_file 1343488
total_swap 0
total_pgpgin 258291419
total_pgpgout 299744842
total_pgfault 1030777333
total_pgmajfault 0
total_inactive_anon 0
total_active_anon 3334144
total_inactive_file 115085312
total_active_file 40202240
total_unevictable 0
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memory soft limit
cat /sys/fs/cgroup/memory/slurm_cn-0008/uid_1023655044/job_14004931/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-0008/uid_1023655044/job_14004931/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-0008/uid_1023655044/job_14004931/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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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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/gpfs/share/apps/jre/7u80/bin/java
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Java Version
java -version 2>&1 | cat
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java version "1.7.0_80"
Java(TM) SE Runtime Environment (build 1.7.0_80-b15)
Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, 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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MRP
mrp --version
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v4.0.5
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mrp templates
ls $(dirname $(dirname $(which mrp)))/jobmanagers/*.template
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