Bowtie-1.2 will not compile with Intel about bowtie HOT 10 OPEN

I will look into and get back to you ASAP.

from bowtie.

Hello,

Has there been any development on supporting the intel compiler?

Thanks,
Greg Zynda

from bowtie.

Hello @zyndagj, @mjarsulic

Apologies for the late response.

I was able to get bowtie compiled on macOS using ICPC albeit with lots of warnings. My (rudimentary) changes are below. I will give Linux a shot tomorrow and post the changes if they are any different, and will also provide an official statement on whether or not we plan on officially supporting ICC/ICPC.

index 65196f0..5f91fd4 100644
--- a/Makefile
+++ b/Makefile
@@ -46,8 +46,8 @@ ifneq (,$(findstring Darwin,$(shell uname)))
MACOS_VER_MAJOR = $(shell uname -r | cut -d. -f1)
MACOS_VER_GT_12 = $(shell [ $(MACOS_VER_MAJOR) -gt 12 ] && echo true)
ifeq (true, $(MACOS_VER_GT_12))

•           CPP = clang++
  

•           CC = clang
  

•           CPP = icpc 
  

•           CC = icc
            override EXTRA_FLAGS += -stdlib=libstdc++
    endif
  

endif
diff --git a/SeqAn-1.1/platform_linux_gcc.h b/SeqAn-1.1/platform_linux_gcc.h
index a385cea..abdfe7b 100644
--- a/SeqAn-1.1/platform_linux_gcc.h
+++ b/SeqAn-1.1/platform_linux_gcc.h
@@ -19,7 +19,7 @@
#define finline inline

// default 64bit type
-typedef int64_t __int64;
+// typedef int64_t __int64;

//define SEQAN_SWITCH_USE_FORWARDS to use generated forwards
diff --git a/SeqAn-1.1/seqan/platform.h b/SeqAn-1.1/seqan/platform.h
index d032011..bc344cc 100644
--- a/SeqAn-1.1/seqan/platform.h
+++ b/SeqAn-1.1/seqan/platform.h
@@ -20,7 +20,7 @@

// default 64bit type
#ifndef __int64
-typedef int64_t __int64;
+// typedef int64_t __int64;
#endif

//define SEQAN_SWITCH_USE_FORWARDS to use generated forwards
diff --git a/processor_support.h b/processor_support.h
index f68ee65..b07d8dd 100644
--- a/processor_support.h
+++ b/processor_support.h
@@ -44,8 +44,8 @@ public:

 try {

#if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) )

•    __cpuid((void *) &regs,0); // test if __cpuid() works, if not catch the exception
  

•    __cpuid((void *) &regs,0x1); // POPCNT bit is bit 23 in ECX
  

•    __cpuid((int *) &regs,0); // test if __cpuid() works, if not catch the exception
  

•    __cpuid((int *) &regs,0x1); // POPCNT bit is bit 23 in ECX
  

#elif defined(USING_GCC_COMPILER)
__get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
#else

from bowtie.

Do you have a separate branch that incorporates these changes? I think the markdown interpreter removed some of the syntax, preventing a patch.

from bowtie.

Sorry about that. I will have the changes (for linux and macOS) pushed to a branch by tomorrow am. I hope that works for you.

from bowtie.

That works! Thanks for the prompt reply.

from bowtie.

I was busy looking into another issue. I am getting started on this right now.

from bowtie.

I pushed the changes to this branch - https://github.com/BenLangmead/bowtie/tree/bt-v1.2.1. The changes are by no means final, and therefore may be revised before the next bowtie release. Your feedback is appreciated.

Thanks

from bowtie.

I can report that I compiled this branch of bowtie using the intel 15 compiler without any warnings with the following commands.

git clone https://github.com/BenLangmead/bowtie.git
cd bowtie
git checkout bt-v1.2.1
make CC=icc CXX=icpc EXTRA_FLAGS="-I${TBBROOT}/include -L${TBBROOT}/lib/intel64/gcc4.4 -xHOST"

I am currently testing the output to make sure alignments are comparable to gcc builds.

from bowtie.

Has anyone tried building Bowtie 1.2.1.1 with the Intel compilers, or do you have suggestions to fix compilation errors like this:

/prefix/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/bits/stl_algobase.h(343): error: no operator "=" matches these operands
            operand types are: HitSink::batch = HitSink::batch
  	      *__result = std::move(*__first);

see also #77 (comment)

from bowtie.