ask about compiling on arm. #12
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You can contact me in Slack or here when you face a problem and I will try to help you resolve it!
The idea is to use more CPU registers simultaneously. By using Neon (for aarch64) and AVX (for 86_64) you can process more data with a single CPU instruction. For example if you have an array of integers and you want to get the sum of them then normally you would use an accumulator (arr[0]) and add to it arr[1], then to the result add arr[2], and so on. Each addition operation would be one CPU cycle. By using SIMD (single instruction - multiple data) you can use several CPU registers for one CPU cycle. For example the accumulator will be the sum of arr[0]+arr[1]+arr[2]+arr[3], then the result will be increased with arr[4]+arr[5]+arr[6]+arr[7], etc.
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Hi, Thank you very much. Here are some questions I'll sort out. |
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The error information is too few to I can see the cause. Would you mind to point out this problem? This is the error report when I use |
No. These files were custom implementation by the PR author. Here is a PR that uses sse2neon - lbcb-sci/graphmap2#23
If you know how to make the improvements then it is better to send a Pull Request! |
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The error is https://bioconductor.org/checkResults/3.18/bioc-LATEST/msa/kunpeng2-checksrc.html uses |
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@yangxingyu588 Let's use Disccussions instead. It supports threading and it will be easier to follow the questions and their answers. |
Thank you, but l can't open this page:https://github.com/bio-arm/bio-arm.github.io/discussions |
What should l do to resolve it. |
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See #14 |
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@yangxingyu588 About AC-DIAMOND: Maihj/AC-DIAMOND#8 |
Hi@martin, I use bioconda-utils build --packages ac-diamond to build ac-diamond However, the build still fails and there are few error messages, could you please help me solve the problem? |
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We will need a need release/tag of AC-DIAMOND to be able to compile it on ARM64. |
diff --git i/recipes/ac-diamond/build.sh w/recipes/ac-diamond/build.sh
index edafd08272..e4702e67cc 100644
--- i/recipes/ac-diamond/build.sh
+++ w/recipes/ac-diamond/build.sh
@@ -1,9 +1,14 @@
mkdir build
cd build
+
+ARCH=$(uname -m)
+if [ ${ARCH} == "x86_64" ]; then
+ARCH_CFLAGS="-msse4.1"
+fi
+
cmake \
-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
- -DCMAKE_CXX_FLAGS="${CXXFLAGS} -msse4.1" \
- -DCMAKE_CXX_STANDARD=98 \
+ -DCMAKE_CXX_FLAGS="${CXXFLAGS} ${ARCH_CFLAGS}" \
..
make
make install
diff --git i/recipes/ac-diamond/meta.yaml w/recipes/ac-diamond/meta.yaml
index c2a63a2ca3..4cedbea4a9 100644
--- i/recipes/ac-diamond/meta.yaml
+++ w/recipes/ac-diamond/meta.yaml
@@ -1,13 +1,13 @@
package:
name: ac-diamond
- version: "1.0"
+ version: "pr8"
source:
- url: https://github.com/Maihj/AC-DIAMOND/archive/v1.0.tar.gz
- sha256: f3ee403390c3de0a2f21f025a45b35c6131f4f39510c834fbe57ade28162c87b
+ url: https://github.com/Maihj/AC-DIAMOND/archive/pr8.tar.gz
+ sha256: 66242fd45f00c71369a441148ce4648d264da7bd6acbd3e09c352c4d93fa9db8
build:
- number: 6
+ number: 0
skip: True # [osx]
requirements:
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Cool, l'm going to try it. l have a question to ask. Some Source code is not compiled on Use |
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One problem that I can see is with reproducibility. If you lose your local modifications it might be hard to re-build the package again if needed. |
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Thank you very much, ac-diamond has built successfully.
yes, you're right, but there are many aarch64 versions that I have simply adapted to that have not been uploaded to the community.
Yes, this is certain. Your adaptation is very cool, it is just an example to illustrate that I used a local file in the |
hi @martin-g @Yikun .What l do now is to use bioconda-utils to build bioconda community software, such as bwa, ac-diamond, etc. l have no foundation, and l often encounter some
makefileandcmakeproblems. l would like to ask what can be referred to in this respect to get started quickly. Thank you very much for your advice.ln addition
cmd is
bioconda-utils build --packages ac-diamondThe text was updated successfully, but these errors were encountered: