Server Processors

[GBIRCHAK]

Hello, I hope you're all doing well. I'm reaching out in an effort to resolve a software incompatibility issue that relates specifically to my CPU (AMD Ryzen Threadripper Pro 5955WX). I am attempting to perform bioinformatics work with the package Samtools within the WSL Ubuntu-20.04 that I'm running on the Windows 10 Pro OS. While I can install the software just fine, whenever I attempt to run a command, I get the following error message: "Please verify that both the operating system and the processor support Intel(R) X87, CMOV, MMX, FXSAVE, SSE, SSE2, SSE3, SSSE3, SSE4_1, SSE4_2 and POPCNT instructions." Indeed, when I execute less /proc/cpuinfo, I see that Intel(R) X87 is missing from the aforementioned flags. Is there a remedy to this problem, such as adding or circumventing the extension?

Thank you for your time!

[AdrianP]

All modern CPU supports x87, but it won't be reflected in cpuinfo since it's ubiquitous. It sounds like at least one component of the software you're running is compiled with the Intel compiler, which will only support SSE on AMD CPUs. If it's MKL, then you can try setting up environment variable MKL_DEBUG_CPU_TYPE=5 as a workaround. If not, then you'll have to recompile the software, which will also provide performance gains if AVX2 support is enabled.

[shrjoshi]

Hello @GBIRCHAK 

Thank you for writing to Serverguru. 
Can you please share the details of compiler and flags used for samtools application?

[GBIRCHAK]

Samtools (https://github.com/samtools/samtools.git) is written in C. At the moment, I haven't installed any compilers myself, but the llvm12 libraries are installed. Perhaps this is my issue. Is there a recommended compiler that I should install? As for the flags, I'm unaware as to how to go about revealing these but would suspect that it's using the flags that are listed in response to my command execution attempts.

[shrjoshi · Accepted solution]

Can you please check by installing AOCC 4.1 released version.
Please refer below links: 
AOCC download link -
https://www.amd.com/en/developer/aocc.html

AOCC User guide - 
https://www.amd.com/content/dam/amd/en/documents/developer/version-4-1-documents/aocc/aocc-4.1-user-...

[GBIRCHAK]

I installed AOCC, which still did not solve the problem. However, I suspected that the issue stemmed from the absence of a compiler during initial installation. So I uninstalled Samtools after installing AOCC and reinstalled it. Now it works like a charm! Thank you so much for the support!