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i have alter gcc version from 4 to 10，but still report an error when I run "make -f Makefile.MIC.icc"

rm -f *.o examl-MIC
mpicc -std=c99 -D__SIM_SSE3 -D_OPTIMIZED_FUNCTIONS -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE -D__MIC_NATIVE -mmic -qopt-streaming-cache-evict=0 -qopenmp -D_USE_OMP -O2 -c -o axml.o axml.c
gcc: error: unrecognized command line option ‘-mmic’; did you mean ‘-fpic’?
gcc: error: unrecognized command line option ‘-qopt-streaming-cache-evict=0’
gcc: error: unrecognized command line option ‘-qopenmp’; did you mean ‘-fopenmp’?
make: *** [axml.o] Error 1

I really don't know how to solve, thank you for your help!

sitesPerProc:

numsPerProc:

destinationUnordered:

Found by Clang's Static Analyzer (LLVM 3.5).

Hi,
there is a bug report in Debian about [quartets.c:393:31: error: implicit declaration of function ‘basename’; did you mean ‘rename’? -Werror=implicit-function-declaration. I've created a patch which fixes the problem.
Kind regards, Andreas.

I was having problems compiling parser-examl with gcc (GCC) 4.9.2 and needed to edit the -msse flag to -msse3 to successfully compile.

diff --git a/parser/Makefile.SSE3.gcc b/parser/Makefile.SSE3.gcc
index a53469e..00f32fa 100644
--- a/parser/Makefile.SSE3.gcc
+++ b/parser/Makefile.SSE3.gcc
@@ -2,7 +2,7 @@
 # Makefile cleanup October 2006, Courtesy of Peter Cordes <[email protected]>

 CC = gcc
-CFLAGS = -fomit-frame-pointer -O2 -D_GNU_SOURCE -msse -funroll-loops  #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-
+CFLAGS = -fomit-frame-pointer -O2 -D_GNU_SOURCE -msse3 -funroll-loops  #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused


 LIBRARIES = -lm

In axml.h, the rawdata->sites variable is defined as type int. Attempting to compress an alignment with about 3B positions is resulting in a "too few sites" error, presumably because we are overflowing the int. We will also have more than 32k site patterns after compression, and some of these will occur more than 32k times in the dataset - so we will still be causing overflows in the site/alias indexes even after changing sites to long long int. Is there a quick fix for this? Thanks!

I installed Examl according to the manual and the parse-examl commands are working, however, if I use the examl command I get this error examl: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory. I found this post theislab/cellrank#864 where a similar error was solved using conda install -c conda-forge openmpi=4.1.2, however this didn't solve the problem for me as the libraries installed are named slightly different libmpi_mpifh.so and libmpi_mpifh.so.40. Any help is appreciated!

I was getting an error "SSE instruction set not enabled" when trying to build the parser on SliTaz linux. Adding -msse to the CFLAGS in the Makefile fixed this.

Best wishes,

Rutger

Hi,
I am a newcomer who is learning about the software. The version I am currently using is 3.0.21. When I use the following command lines to run on the same cluster, I get an error.

command lines:
./ExaML-master/parser/parse-examl -s data/dna_rokasD1/dna_rokasD1.phy -q data/dna_rokasD1/dna_rokasD1.model -m DNA -n dna_rokasD1

./ExaML-master/examl/examl-AVX -m GAMMA -n ex_dna_rokasD1_p1 -s data/dna_rokasD1/dna_rokasD1.phy -t data/dna_rokasD1/start_trees/start_p1 -w data/dna_rokasD1

error: the address data type has a size of 64 bits on the current system while on the system on which you created the binary alignment file using the parser the address size is -910573176 bits!
Usually this indicates that the parser was executed on a 32-bit system while you are trying to run ExaML on a 64-bit system.
Please parse the binary alignment file on the same hardware on which you intend to run ExaML.

But I am using the same cluster. I do not know why this is so. Thanks in advance if you can help me.

Kind regards,
Cynthia

HI，
I want to test the examl in Arm architecture v8 cpu, how to compile the examl program ?

Hi,

I am getting an error but not sure what it means:

Examl-OMP-AVX: treeIO.c:907: treeReadLen: Assertion `tr->ntips == tr->mxtips' failed.
[s4:161245] *** Process received signal ***
[s4:161245] Signal: Aborted (6)
[s4:161245] Signal code: (-6)
[s4:161245] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10330) [0x7f257a1b2330]
[s4:161245] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37) [0x7f2579e10c37]
[s4:161245] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x7f2579e14028]
[s4:161245] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2fbf6) [0x7f2579e09bf6]
[s4:161245] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2fca2) [0x7f2579e09ca2]
[s4:161245] [ 5] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x424810]
[s4:161245] [ 6] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x4252b2]
[s4:161245] [ 7] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x4047a6]
[s4:161245] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f2579dfbf45]
[s4:161245] [ 9] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x404987]
[s4:161245] *** End of error message ***
Aborted (core dumped)

The command I am running is this:

raxmlHPC-PTHREADS-AVX -y -m GTRCAT -p 12345 -s all_samples.phylip -n StartingTree -T 40
parse-examl -s all_samples.phylip -n all_samples -m DNA
examl-OMP-AVX -s all_samples.binary -n examl -m PSR -D -t RAxML_parsimonyTree.StartingTree

RAxML runs fine but ExaML throws an error...
Any ideas on how to troubleshoot?

Thanks,
Jody