cellranger  (cellranger-9.0.1)
Copyright 2023 10x Genomics, Inc. All rights reserved.
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Wed Mar 12 09:07:09 PDT 2025

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System Info
uname -a
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Linux sh02-05n39.int 3.10.0-1160.119.1.el7.tuxcare.els14.x86_64 #1 SMP Mon Jan 20 19:06:00 UTC 2025 x86_64
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CPU Model
grep -m 1 'model name' /proc/cpuinfo | cut -d ':' -f 2 | sed 's/^[ 	]*//'
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Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
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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 7.9.2009 (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"
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Kernel Build
cat /proc/version
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Linux version 3.10.0-1160.119.1.el7.tuxcare.els14.x86_64 (mockbuild@buildfarm08-new.corp.cloudlinux.com) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) ) #1 SMP Mon Jan 20 19:06:00 UTC 2025
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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 Support
grep -m 1 'flags' /proc/cpuinfo | cut -d ':' -f 2 | sed '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 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 ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap intel_pt xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts md_clear spec_ctrl intel_stibp flush_l1d
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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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20
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Memory Total
grep MemTotal /proc/meminfo | cut -d ':' -f 2 | sed 's/^[ 	]*//'
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263777836 kB
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Filesystem Options
mount | cut -d ' ' -f 5,6
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xfs (rw,relatime)
devtmpfs (rw,nosuid)
tmpfs (rw,nosuid,nodev)
devpts (rw,nosuid,noexec,relatime)
mqueue (rw,relatime)
hugetlbfs (rw,relatime)
proc (rw,nosuid,nodev,noexec,relatime)
autofs (rw,relatime)
binfmt_misc (rw,relatime)
sysfs (rw,nosuid,nodev,noexec,relatime)
securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs (ro,nosuid,nodev,noexec)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
cgroup (rw,nosuid,nodev,noexec,relatime)
pstore (rw,nosuid,nodev,noexec,relatime)
efivarfs (rw,nosuid,nodev,noexec,relatime)
configfs (rw,relatime)
debugfs (rw,relatime)
tmpfs (rw,nosuid,nodev)
ext4 (rw,relatime)
vfat (rw,relatime)
xfs (rw,nosuid,relatime)
rpc_pipefs (rw,relatime)
nfs (ro,nosuid,noatime)
nfs (ro,nosuid,noatime)
autofs (rw,relatime)
nfs4 (rw,nosuid,relatime)
autofs (rw,relatime)
lustre (rw,nosuid)
lustre (rw,nosuid)
xfs (rw,nosuid,relatime)
xfs (rw,nosuid,relatime)
tmpfs (rw,nosuid,nodev)
nfs4 (rw,nosuid,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) 1029646
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) 274877906944
open files                      (-n) 131072
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) 10240
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited
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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) 1029646
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) 274877906944
open files                      (-n) 131072
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) 1029646
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited
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Global File Limit
cat /proc/sys/fs/file-max /proc/sys/fs/file-nr
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25998291
2320	0	25998291
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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 = 1048576
vm.memory_failure_early_kill = 0
vm.memory_failure_recovery = 1
vm.min_free_kbytes = 524288
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 = 0
vm.user_reserve_kbytes = 131072
vm.vfs_cache_pressure = 50
vm.zone_reclaim_mode = 1
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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:memory:/slurm/uid_312359/job_61258961/step_interactive/task_0
10:cpuset:/slurm/uid_312359/job_61258961/step_interactive/task_0
9:pids:/system.slice/slurmd.service
8:perf_event:/
7:blkio:/system.slice/slurmd.service
6:freezer:/slurm/uid_312359/job_61258961/step_interactive
5:devices:/slurm/uid_312359/job_61258961/step_interactive/task_0
4:net_prio,net_cls:/
3:hugetlb:/
2:cpuacct,cpu:/slurm/uid_312359/job_61258961/step_interactive/task_0
1:name=systemd:/system.slice/slurmd.service
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cgroup mem stats
cat /sys/fs/cgroup/memory/slurm/uid_312359/job_61258961/step_interactive/task_0/memory.stat
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cache 1031278592
rss 5627904
rss_huge 0
mapped_file 2625536
swap 0
pgpgin 7839201
pgpgout 7586050
pgfault 10378629
pgmajfault 7218
inactive_anon 0
active_anon 5484544
inactive_file 782929920
active_file 248348672
unevictable 0
hierarchical_memory_limit 68719476736
hierarchical_memsw_limit 68719476736
total_cache 1031278592
total_rss 5627904
total_rss_huge 0
total_mapped_file 2625536
total_swap 0
total_pgpgin 0
total_pgpgout 0
total_pgfault 0
total_pgmajfault 0
total_inactive_anon 0
total_active_anon 5484544
total_inactive_file 782929920
total_active_file 248348672
total_unevictable 0
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memory soft limit
cat /sys/fs/cgroup/memory/slurm/uid_312359/job_61258961/step_interactive/task_0/memory.soft_limit_in_bytes /sys/fs/cgroup/memory/slurm/uid_312359/job_61258961/step_interactive/task_0/memory.memsw.soft_limit_in_bytes
---------------------------------------------------------------------
9223372036854771712
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memory hard limit
cat /sys/fs/cgroup/memory/slurm/uid_312359/job_61258961/step_interactive/task_0/memory.limit_in_bytes
---------------------------------------------------------------------
9223372036854771712
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memory swap limit
cat /sys/fs/cgroup/memory/slurm/uid_312359/job_61258961/step_interactive/task_0/memory.memsw.limit_in_bytes
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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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SGE Submit
which qsub
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LSF Submit
which bsub
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HTCondor Submit
which condor_submit
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Batch system
echo $BATCH_SYSTEM
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BCL2FASTQ 1
which configureBclToFastq.pl
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BCL2FASTQ 1
which bcl2fastq
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Java
which java
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/share/software/user/open/java/1.8.0_131/bin/java
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Java Version
java -version 2>&1 | cat
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java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)
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10X Refdata
echo $TENX_REFDATA
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slurm info
sinfo -O nodes,maxcpuspernode,memory,time
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NODES               MAX_CPUS_PER_NODE   MEMORY              TIMELIMIT           
324                 UNLIMITED           128000+             7-00:00:00          
11                  UNLIMITED           384000+             1-00:00:00          
4                   UNLIMITED           128000+             2:00:00             
1557                UNLIMITED           128000+             2-00:00:00
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MRP
mrp --version
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v4.0.13
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mrp templates
ls $(dirname $(dirname $(which mrp)))/jobmanagers/*.template
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