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Megahit in Arm Neoverse de 64 bits core #320

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higaredavm opened this issue Dec 3, 2021 · 9 comments · May be fixed by #368
Open

Megahit in Arm Neoverse de 64 bits core #320

higaredavm opened this issue Dec 3, 2021 · 9 comments · May be fixed by #368

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@higaredavm
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We are exploring bioinformtics in amazon AWS, specifically we want to run genome assembly on AWS Graviton2 processors which have an ARM architecture. Is there a version of megahit built for ARM / aarch64 architecture.
@aclum
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aclum commented Dec 3, 2021

We have had good success with graviton2 with other bioinformatics tools and would also be interested of a version of megathit which compiles on ARM.

@higaredavm
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We have had good success with graviton2 with other bioinformatics tools and would also be interested of a version of megathit which compiles on ARM.

I am curious about what bioinformatics tools have you been running on graviton2.

@aclum
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aclum commented Dec 3, 2021

From BBTools, BBMap and BBcms both run on graviton2. These are AWS blog posts on peregrine and bwa on graviton2
https://aws.amazon.com/blogs/publicsector/accelerating-genome-assembly-aws-graviton2/
https://aws.amazon.com/blogs/publicsector/generalized-approach-benchmarking-genomics-workloads-cloud-bwa-read-aligner-graviton2/

@aclum
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aclum commented Dec 17, 2021

I made some progress on getting MEGAHIT working on ARM but am stalled on the third issue

The first issue is with x86 specific flags (-mbmi2 & -mpopcnt) which can be removed from the CMakeLists.txt file.

The second issue is with x86intrin.h and can be fixed by replacing with openvec*.h files from https://github.com/OpenVec/OpenVec

The third issue is an error about "impossible constraint in ‘asm’". Based on searching stack overflow this can be fixed by rewriting the code in c++ instead of assembly
https://stackoverflow.com/questions/1478513/linux-assembler-error-impossible-constraint-in-asm

Would it be possible to get the third issue fixed?

@voutcn
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voutcn commented Mar 24, 2022

You can just replace

megahit/src/utils/cpu_dispatch.h

Lines 8 to 34 in 7dde1ca

inline bool HasPopcnt() {
unsigned eax, ebx, ecx, edx;
#ifdef _MSC_VER
int cpuid[4];
__cpuid(cpuid, 1);
eax = cpuid[0], ebx = cpuid[1], ecx = cpuid[2], edx = cpuid[3];
#else
asm volatile("cpuid\n\t"
: "=a"(eax), "=b"(ebx), "=c"(ecx), "=d"(edx)
: "0"(1));
#endif
return ecx >> 23U & 1U;
}
inline bool HasBmi2() {
unsigned eax, ebx, ecx, edx;
#ifdef _MSC_VER
int cpuid[4];
__cpuidex(cpuid, 7, 0);
eax = cpuid[0], ebx = cpuid[1], ecx = cpuid[2], edx = cpuid[3];
#else
asm volatile("cpuid\n\t"
: "=a"(eax), "=b"(ebx), "=c"(ecx), "=d"(edx)
: "0"(7), "2"(0));
#endif
return ebx >> 8U & 1U;
}

with

inline bool HasPopcnt() { return false; }
inline bool HasBmi2() { return false; }

I don't have an Arm machine to test. Let me know if that works. Also feel free to send a PR.

@aquaskyline to follow up.

@accopeland
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For the record, the above suggestions are sufficient to compile megahit on graviton2. I am working on a PR.

@aquaskyline aquaskyline mentioned this issue Mar 31, 2022
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@higaredavm
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@voutcn We are doing the changes that you suggest, however we are having this error. I really appreciate your help, thanks
image-2

@voutcn
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voutcn commented Apr 5, 2022

I think the error has nothing to do with ARM. One *.edges.info file is broken for some unknown reason. Could you retry?

martin-g added a commit to martin-g/megahit that referenced this issue Mar 27, 2024
@martin-g
Add support for non-x86_64 architectures (e.g. Linux ARM64)
296ad6b 
Fixes voutcn#320
Based on: voutcn#329

Preserves the x86_64 specifics when building on x86_64 machine

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@martin-g martin-g linked a pull request Mar 27, 2024 that will close this issue
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@martin-g
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Hi!

I created a new PR - #368
It is built on top of #329 but preserves the x86_64 optimizations.

martin-g added a commit to martin-g/megahit that referenced this issue Apr 4, 2024
@martin-g
Add support for non-x86_64 architectures (e.g. Linux ARM64)
4687e4f 
Fixes voutcn#320
Based on: voutcn#329

Preserves the x86_64 specifics when building on x86_64 machine

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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Add support for non-x86_64 architectures (e.g. Linux ARM64) martin-g/megahit
5 participants
@martin-g @accopeland @voutcn @aclum @higaredavm