Illegal instruction (core dumped)

[kOoLiNuS]

Ciao ! On a fresh MAESTRO — release 1.5.1 — installation (Ubuntu 18.04 with Python v3.8.12 installed) I tried to run chromap, chromap --version or chromap -h having immediately Illegal instruction (core dumped) as a result.

I did also try to update chromap with conda install -c bioconda chromap obtaining chromap-0.1.5-h9a82719_0 with no error during installation but, again the Illegal instruction error happened.

What can I do? Thanks

[haowenz]

What is your CPU specification? Can you run cat /proc/cpuinfo and more /proc/cpuinfo | grep flags and share the output of these two commands with us?

[kOoLiNuS]

update #1 = with the MAESTRO env enabled I do have:

$ whereis chromap chromap: /opt/mambaforge/bin/chromap /opt/mambaforge/envs/MAESTRO/bin/chromap

The first one (installed with bioconda, given the path) works ok.

[kOoLiNuS]

koolinus@machine:~$ cat /proc/cpuinfo

processor	: 0
vendor_id	: GenuineIntel
cpu family	: 6
model		: 45
model name	: Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
stepping	: 7
microcode	: 0x71a
cpu MHz		: 1197.109
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 cpuid aperfmperf 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 pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid xsaveopt dtherm ida arat pln pts md_clear flush_l1d
bugs		: cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds swapgs itlb_multihit
bogomips	: 4788.48
clflush size	: 64
cache_alignment	: 64
address sizes	: 46 bits physical, 48 bits virtual
power management:

…

processor	: 63
vendor_id	: GenuineIntel
cpu family	: 6
model		: 45
model name	: Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
stepping	: 7
microcode	: 0x71a
cpu MHz		: 1196.972
cache size	: 20480 KB
physical id	: 3
siblings	: 16
core id		: 7
cpu cores	: 8
apicid		: 111
initial apicid	: 111
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 cpuid aperfmperf 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 pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid xsaveopt dtherm ida arat pln pts md_clear flush_l1d
bugs		: cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds swapgs itlb_multihit
bogomips	: 4807.33
clflush size	: 64
cache_alignment	: 64
address sizes	: 46 bits physical, 48 bits virtual
power management:

and

koolinus@machine:~$ more /proc/cpuinfo | grep flags

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 cpuid aperfmperf 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 pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid xsaveopt dtherm ida arat pln pts md_clear flush_l1d

here's the Intel specs for my E5-4640 CPU

[haowenz]

Ok. Since the first one works and your CPU seems normal, I think it is MAESTRO environment problem rather than Chromap problem. Maybe you can start an issue in MAESTRO repo.

[kOoLiNuS]

I've done this too … I wrote also here because the MAESTRO installation went OK with no error at al (and other programs provided works as expected).

THANKS