I tried to run the code above, but the hhblits always stopped when prefiltering database. After checking, the task is found to be asleep.
When look into the job with strace -p JobID, showed this:
strace: Process 85754 attached
sched_yield() = 0
sched_yield() = 0
sched_yield() = 0
sched_yield() = 0
sched_yield() = 0
sched_yield() = 0
sched_yield() = 0
Steps to Reproduce (for bugs)
Log info:
HH-suite Output (for bugs)
19:04:07.440 INFO: Search results will be written to A0A0K3ARH1.hhr
19:04:56.810 INFO: Searching 32053680 column state sequences.
19:04:56.923 INFO: A0A0K3ARH1.fa is in A2M, A3M or FASTA format
19:04:56.924 INFO: Iteration 1
19:04:57.018 INFO: Prefiltering database
Context
Size of the UniRef30_2022_02 -oa3m database is 180G, and the server RAM is 250G. Could the RAM cause the job to go to sleep, or other potential reasons?
:exclamation: Make to check out our User Guide.
Expected Behavior
hhblits -cpu 20 -i A0A0K3ARH1.fa -d /work/home/ac1daawz21/software/DPAM-main/DPAM/UniRef30_2022_02/UniRef30_2022_02 -oa3m A0A0K3ARH1.a3mCurrent Behavior
I tried to run the code above, but the
hhblitsalways stopped when prefiltering database. After checking, the task is found to be asleep.When look into the job with
strace -p JobID, showed this: strace: Process 85754 attached sched_yield() = 0 sched_yield() = 0 sched_yield() = 0 sched_yield() = 0 sched_yield() = 0 sched_yield() = 0 sched_yield() = 0Steps to Reproduce (for bugs)
Log info: HH-suite Output (for bugs)
19:04:07.440 INFO: Search results will be written to A0A0K3ARH1.hhr
19:04:56.810 INFO: Searching 32053680 column state sequences.
19:04:56.923 INFO: A0A0K3ARH1.fa is in A2M, A3M or FASTA format
19:04:56.924 INFO: Iteration 1
19:04:57.018 INFO: Prefiltering database
Context
Size of the UniRef30_2022_02 -oa3m database is 180G, and the server RAM is 250G. Could the RAM cause the job to go to sleep, or other potential reasons?
Your Environment
Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge aria2 1.36.0 h8b6cd97_3 conda-forge bzip2 1.0.8 h7b6447c_0
c-ares 1.19.0 h5eee18b_0
ca-certificates 2023.01.10 h06a4308_0
certifi 2020.6.20 pyhd3eb1b0_3
dssp 2.2.1 1 ostrokach foldseek 5.53465f0 pl5321hf1761c0_0 bioconda gawk 5.1.0 h7b6447c_0
hhsuite 3.3.0 py36pl5321h4aaaa08_5 bioconda icu 58.2 he6710b0_3
ld_impl_linux-64 2.38 h1181459_1
libffi 3.3 he6710b0_2
libgcc-ng 12.2.0 h65d4601_19 conda-forge libidn2 2.3.2 h7f8727e_0
libnsl 2.0.0 h5eee18b_0
libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libunistring 0.9.10 h27cfd23_0
libxml2 2.10.3 hcbfbd50_0
libzlib 1.2.13 h166bdaf_4 conda-forge llvm-openmp 14.0.6 h9e868ea_0
ncurses 6.4 h6a678d5_0
openssl 1.1.1t h7f8727e_0
pdbx 1.0.0 py36_0 ostrokach-forge perl 5.32.1 2_h7f98852_perl5 conda-forge pip 20.0.2 py36_1 conda-forge python 3.6.13 h12debd9_1
python_abi 3.6 2_cp36m conda-forge readline 8.2 h5eee18b_0
setuptools 49.6.0 py36h5fab9bb_3 conda-forge sqlite 3.41.1 h5eee18b_0
tk 8.6.12 h1ccaba5_0
wget 1.21.3 h0b77cf5_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.10 h5eee18b_1
zlib 1.2.13 h166bdaf_4 conda-forge
server info:
Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 64 On-line CPU(s) list: 0-63 Thread(s) per core: 1 Core(s) per socket: 32 Socket(s): 2 NUMA node(s): 8 Vendor ID: HygonGenuine CPU family: 24 Model: 1 Model name: Hygon C86 7285H 32-core Processor Stepping: 1 CPU MHz: 2500.000 CPU max MHz: 2500.0000 CPU min MHz: 1200.0000 BogoMIPS: 5000.05 Virtualization: AMD-V L1d cache: 32K L1i cache: 64K L2 cache: 512K L3 cache: 8192K NUMA node0 CPU(s): 0-7 NUMA node1 CPU(s): 8-15 NUMA node2 CPU(s): 16-23 NUMA node3 CPU(s): 24-31 NUMA node4 CPU(s): 32-39 NUMA node5 CPU(s): 40-47 NUMA node6 CPU(s): 48-55 NUMA node7 CPU(s): 56-63 Flags: 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 art rep_good nopl nonstop_tsc extd_apicid amd_dcm aperfmperf eagerfpu pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_l2 hw_pstate sme retpoline_amd ssbd ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca