Is the old "bonus score" still available in version 3?
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@TimoLassmann I am updating Kalign at EMBL-EBI and I was trying to find the "bonus score" option (-m in kalign v2) but can't find it in the source code. Likely missing it, though...
Hi,
For some reason I re-named this option "matadd". However, this option is actually no longer required. Default options will work fine in almost all cases and for the EMBL-EBI interface I would think that offering the options for gap open , gap extension and terminal gap extensions are sufficient. Thanks, T
@TimoLassmann Thanks! I will update the service shortly, but somehow I am struggling with an issue in our setup when running with Singularity. It installs fine via source or linuxbrew (see PR), but fails with "Illegal instruction" in some runs. Hopefully will fix it shortly and have version 3 up and running for everyone!
Hmm .. never encountered a fail with "Illegal instruction". Could you send me a reproducible example of the error case together with the inputs?
It's not an issue with Kalign, but rather an issue with running the container with Singularity in our infrastructure. I think I have it working now, just need to deploy it for further testing...
Thanks a lot for your help and I will be in touch when it is live :)
Great - thanks for the work you are putting into this - appreciated!
@TimoLassmann it turns out kalign is working great in some of our machines but fails with "Illegal instruction" on some others... I have asked for help from our Sys Admins, but I wonder if it would be possible to get static binaries for this version? Not sure if it would fix it but is generally how we are running some of the tools as they are only provided pre-built.
Could you send me more information - what CPUs are used on the machines on which kalign works and machines in which it fails (cat /proc/cpuinfo) ? Is there additional information in addition to the "Illegal instruction" message? I have a suspicion that this relates to AVX2 instructions and the way my configure script checks for the presence of them. Naturally, I would prefer to identify the root cause for these errors, also for the benefit of other users.
No problem and thanks!
I was not sure what the error related to because I am running kalign with Singularity. The output when it fails is simply
Kalign (3.3.1)
Copyright (C) 2006,2019,2020,2021 Timo Lassmann
This program comes with ABSOLUTELY NO WARRANTY; for details type:
`kalign -showw'.
This is free software, and you are welcome to redistribute it
under certain conditions; consult the COPYING file for details.
Please cite:
Lassmann, Timo.
"Kalign 3: multiple sequence alignment of large data sets."
Bioinformatics (2019)
https://doi.org/10.1093/bioinformatics/btz795
Illegal instruction
two examples of cpuinfo for the machines that work:
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 79
model name : Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2200.000
cache size : 25600 KB
physical id : 0
siblings : 20
core id : 0
cpu cores : 10
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 20
wp : yes
flags : 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 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 tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips : 4394.97
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 63
model name : Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz
stepping : 2
microcode : 0x3a
cpu MHz : 2600.000
cache size : 25600 KB
physical id : 0
siblings : 20
core id : 0
cpu cores : 10
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 15
wp : yes
flags : 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 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm epb invpcid_single tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc dtherm ida arat pln pts
bogomips : 5194.14
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
two examples cpuinfo for machines that don't work:
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 45
model name : Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
stepping : 7
microcode : 0x710
cpu MHz : 2600.000
cache size : 20480 KB
physical id : 0
siblings : 16
core id : 0
cpu cores : 8
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : 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 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm epb tpr_shadow vnmi flexpriority ept vpid xsaveopt dtherm ida arat pln pts
bogomips : 5200.34
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 62
model name : Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
stepping : 4
microcode : 0x428
cpu MHz : 2600.000
cache size : 20480 KB
physical id : 0
siblings : 16
core id : 0
cpu cores : 8
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : 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 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm epb tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts
bogomips : 5199.91
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
Thanks for sending this through - the two machines on which kalign doesn't work don't have the AVX2 instruction set. I suspect you compiled / built the container on a machine with AVX2.
It would be ideal to run kalign on the machines with AVX2 for production. I have to note that the other two processors appear to be rather venerable (released almost a decade ago).
Thanks @TimoLassmann! I noticed that as well! I will request SysAdmins to run kalign from the newer machines.
Kind regards,
Fábio