compilation in Linux 64bit

mothur bugs
1

Hi,
I follow the the wiki page for mothur 1.13 installation in linux 64bit:
http://www.mothur.org/wiki/Installation
I edit the makefile, but there is no such line as:

CC_OPTIONS = -O3

do I need only change the CXXFLAGS line ?
it doesn’t really clear what do I need to change there for version 1.13
Thanks.

2

no idea about that.
sorry.

3

Yes, you want CXXFLAGS. Sorry for the confusion, it seems we need to update the installation wiki page, :oops: . FYI, we are planning on releasing version 1.14.0 later today, if you want to wait and grab the latest version.

4

Thanks,
so, for version 1.13/1.14 I need to change:
CXXFLAGS += -O3
to:
CXXFLAGS += -O3 -m64
that’s all ?

5

Version 1.14.0 has a few more modifications to the makefile. I have made the modifications to the makefile you will need to make in the new version below. You may also want to set the default directory, and set USEREADLINE ?= no if you do not have the readline libraries installed. I will work on updating the wiki installation instructions soon.

CXXFLAGS += -O3

64BIT_VERSION ?= yes

ifeq ($(strip $(64BIT_VERSION)),yes)
#if you are using centos uncomment the following lines
#CXX = g++44

#if you are a mac user use the following line
#TARGET_ARCH += -arch x86_64

#if you are a linux user use the following line
CXXFLAGS += -mtune=native -march=native -m64

CXXFLAGS += -DBIT_VERSION
endif

MOTHUR_FILES ="“Enter_your_default_path_here”"

RELEASE_DATE = "“10/26/2010"”
VERSION = "“1.14.0"”

CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}

ifeq ($(strip $(MOTHUR_FILES)),"“Enter_your_default_path_here”")
else
CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
endif

CYGWIN_BUILD ?= no
ifeq ($(strip $(CYGWIN_BUILD)),yes)
CXXFLAGS += -mno-cygwin
LDFLAGS += -mno-cygwin
endif

if you do not want to use the readline library, set this to no.

make sure you have the library installed

USEREADLINE ?= yes

ifeq ($(strip $(USEREADLINE)),yes)
CXXFLAGS += -DUSE_READLINE
LIBS =
-lreadline
-lncurses
endif

USEMPI ?= no

ifeq ($(strip $(USEMPI)),yes)
CXX = mpic++
CXXFLAGS += -DUSE_MPI
endif

if you want to enable reading and writing of compressed files, set to yes.

The default is no. this may only work on unix-like systems.

USECOMPRESSION ?= no

ifeq ($(strip $(USECOMPRESSION)),yes)
CXXFLAGS += -DUSE_COMPRESSION
endif

…

6

Version 1.14.0 is up on the wiki. If you aren’t tailoring your build, you may want to try the Linux executable.

7

Hi,
I’m trying to compile mothur 14.0 MPI-enabled on linux cluster system.
I’ve enable 64-bit architecture, readline, compression, and MPI.

i get many of the following errors:

[b]icpc: command line warning #10159: invalid argument for option ‘-m’

mothurout.cpp(525): warning #68: integer conversion resulted in a change of sign
if (path.rfind("./") == -1) { return fileName; } //already complete name[/b]

but the following error kills the compilation process:

compilation aborted for mothurout.cpp (code 2)
make: *** [mothurout.o] Error 2

I’ve compiled with MPI previously (using version 13.0) but never with compilation…any suggestions?

Thanks

8

hi,
I re-compiled without compression enabled and it seems the compilation ran to completion. Is there a bug associated with the compression option?

Thanks