Problem on compiling RAxML (make -f Makefile.gcc)

[Wai Yan Choi]

Hello, everyone, I am now conducting my final year project, and new to programming, I encountered problems in compiling RAxML by receiving 

error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);

what should I do? Thank you very much!

(I am using Terminal)

[Wai Yan Choi]

I also tried with make -f Makefile.AVX.gcc

[Alexandros Stamatakis]

On what kind of computer are you trying to compile the code?

Is it a Linux system or a MAC?

Is it an x86 or an ARM processor?

I would assume there might also be some problem with your compiler
installation, it's unclear to me at least why you are getting warnings
related top clang while using gcc.

Alexis

On 22.04.22 04:03, Wai Yan Choi wrote:
>
> Screenshot 2022-04-22 at 10.02.51 AM.png
> I also tried with make -f Makefile.AVX.gcc
> On Friday, April 22, 2022 at 9:59:36 AM UTC+8 Wai Yan Choi wrote:
>
> Hello, everyone, I am now conducting my final year project, and new
> to programming, I encountered problems in compiling RAxML by receiving
>

> *error: **invalid conversion between vector type '__m64' (vector of

> 1 'long long' value) and integer type 'int' of different size

> *return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);

>
> what should I do? Thank you very much!
>
> (I am using Terminal)
>

> Screenshot 2022-04-22 at 9.58.15 AM.png
>

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org

[Anne Jarrell]

Hi, 

I am not the original poster, but I am running into the exact same issue. I downloaded the standard RaxML zip file from GitHub as of this week and I am trying to compile on a new MAC that has an ARM processor (Apple M1 chip), if that helps. I have tried compiling with and without AVX and SSE3 as well as .mac and .gcc files, and everything throws the same error. 

Anne Frances

[Alexandros Stamatakis]

Hi Anne,

Thanks a lot.

Okay, the problem is the ARM processor then I guess.

Does executing:

rm *.o
make -f Makefile.gcc

also not work?

Please not that standard RAxML is not supported any more, but you should
switch to RAxML-NG:

https://github.com/amkozlov/raxml-ng

If you absolutely want to use standard RAxML, then the MAC expert in our
lab could have a look at this I guess.

It is most probably connected with the <xmmintrin.h> header files
included in the source code.

Alexis


On 06.05.22 06:54, Anne Jarrell wrote:
> Image 5-5-22 at 11.51 PM.jpgHi,

> <https://groups.google.com/d/msgid/raxml/c1df3397-e228-45f3-a3d6-e3522191ee11n%40googlegroups.com?utm_medium=email&utm_source=footer

> <https://groups.google.com/d/msgid/raxml/c1df3397-e228-45f3-a3d6-e3522191ee11n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP)
> lab,
> Institute of Molecular Biology and Biotechnology, Foundation for
> Research and Technology Hellas
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>

>
> --
> You received this message because you are subscribed to the Google
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> To unsubscribe from this group and stop receiving emails from it, send
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> <https://groups.google.com/d/msgid/raxml/8dc89c51-9a79-4309-b1d9-c816883b5ea1n%40googlegroups.com?utm_medium=email&utm_source=footer>.

[Anne Jarrell]

Hi Alexis, 

Correct, executing rm *.o then make -f Makefile.gcc does not work. The only reason I'm using standard RAxML instead of RAxML-NG is because I am doing a final project for a class and the professor specified to use standard RAxML. Thanks for the help, I really appreciate it! 

Anne Frances

[Alexey Kozlov]

Hi Anne,

on M1 macs, you will need to compile and run RAxML in x86 emulation mode (Rosetta), please see:

https://osxdaily.com/2020/11/18/how-run-homebrew-x86-terminal-apple-silicon-mac/

Best,
Alexey

On 06.05.22 16:17, Anne Jarrell wrote:
> Hi Alexis,
>
> Correct, executing rm *.o then make -f Makefile.gcc does not work. The only reason I'm using
> standard RAxML instead of RAxML-NG is because I am doing a final project for a class and the
> professor specified to use standard RAxML. Thanks for the help, I really appreciate it!
>
> Anne Frances
>
>
> On Friday, May 6, 2022 at 6:10:28 AM UTC-4 Alexis wrote:
>
> Hi Anne,
>
> Thanks a lot.
>
> Okay, the problem is the ARM processor then I guess.
>
> Does executing:
>
> rm *.o
> make -f Makefile.gcc
>
> also not work?
>
> Please not that standard RAxML is not supported any more, but you should
> switch to RAxML-NG:
>

> https://github.com/amkozlov/raxml-ng <https://github.com/amkozlov/raxml-ng>

> > www.exelixis-lab.org <http://www.exelixis-lab.org> <http://www.exelixis-lab.org

> <http://www.exelixis-lab.org>>
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> > an email to raxml+un...@googlegroups.com
> > <mailto:raxml+un...@googlegroups.com>.
> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/raxml/8dc89c51-9a79-4309-b1d9-c816883b5ea1n%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/8dc89c51-9a79-4309-b1d9-c816883b5ea1n%40googlegroups.com>
> >

> <https://groups.google.com/d/msgid/raxml/8dc89c51-9a79-4309-b1d9-c816883b5ea1n%40googlegroups.com?utm_medium=email&utm_source=footer

> <https://groups.google.com/d/msgid/raxml/8dc89c51-9a79-4309-b1d9-c816883b5ea1n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
> Institute of Molecular Biology and Biotechnology, Foundation for
> Research and Technology Hellas
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
> --
> You received this message because you are subscribed to the Google Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to
> raxml+un...@googlegroups.com <mailto:raxml+un...@googlegroups.com>.
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> <https://groups.google.com/d/msgid/raxml/6a33dcc9-a1ae-4703-851e-f7fc9bb50f7en%40googlegroups.com?utm_medium=email&utm_source=footer>.

[Victor Lin]

I was able to compile on an M1 mac with a few changes. This should work:

git clone --recurse-submodules --single-branch --branch simde https://github.com/victorlin/standard-RAxML.git

cd standard-RAxML

make -f Makefile.AVX.PTHREADS.gcc

See this PR comment for more info.

–

Victor Lin

Full Stack Developer

Fred Hutchinson Cancer Center | Bedford Lab | Nextstrain