# Mothur MPI make error

**URL:** <https://forum.mothur.org/t/mothur-mpi-make-error/3133>\
**Category:** Integrating mothur with other programs\
**Created:** [February 19, 2017, 10:16pm UTC](https://forum.mothur.org/t/mothur-mpi-make-error/3133 "2017-02-19T22:16:51Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![heyheyhey](https://avatars.discourse-cdn.com/v4/letter/h/da6949/32.png) [@heyheyhey](https://forum.mothur.org/u/heyheyhey)\
**Post date:** [February 19, 2017, 10:16pm UTC](https://forum.mothur.org/t/mothur-mpi-make-error/3133/1 "2017-02-19T22:16:51Z")

</div>

Hi,

(Wasn’t sure what topic to put this under.)

I’ve been trying to install MPI Mothur, but I can’t get past the ‘make’ command.  
_\*\*Note: I can’t put anything into /usr/local (I don’t have permissions)_

So far I’ve…

```plaintext
wget http://sourceforge.net/projects/boost/files/boost/1.63.0/boost_1_63_0.tar.gz
$ tar -zxvf /home/mpiuser/bin/boost_1_51_0.tar.gz
$ cd boost_1_51_0
$ ./bootstrap.sh --prefix="/home/mpiuser/bin"
added 'using mpi ;' to the /home/mpiuser/bin/boost_1_63_0/project-config.jam
$ ./b2

```

It looks like I get a clean install.

> The Boost C++ Libraries were successfully built!

> The following directory should be added to compiler include paths:

> /home/mpiuser/bin/boost\_1\_63\_0

> The following directory should be added to linker library paths:

> /home/mpiuser/bin/boost\_1\_63\_0/stage/lib

I go ahead and export the paths…

```plaintext
$ export COMPILER_PATH="/home/mpiuser/bin/boost_1_63_0"
$ echo $COMPILER_PATH
/home/mpiuser/bin/boost_1_63_0

$ export LIBRARY_PATH="/home/mpiuser/bin/boost_1_63_0/stage/lib"
$ echo $LIBRARY_PATH
/home/mpiuser/bin/boost_1_63_0/stage/lib

```

I navigate back to the mothur directory. /home/mpiuser/mothur-1.39.2  
\_I got the download from [https://github.com/mothur/mothur/archive/v1.39.2.tar.gz\_](https://github.com/mothur/mothur/archive/v1.39.2.tar.gz_)

I go to edit the Makefile to alter the paths.

```plaintext
BOOST_LIBRARY_DIR="\"/home/mpiuser/bin/boost_1_63_0/lib/\""
BOOST_INCLUDE_DIR="\"/home/mpiuser/bin/boost_1_63_0/include\""

```

I notice there is no USEMPI variable to change to ‘yes’ like this manual suggests.

> **[Makefile options](https://mothur.org/wiki/Makefile_options)**
>
> The website that supports the mothur software program - one of the most widely used tools for analyzing 16S rRNA gene sequence data. Step inside to learn how to use the software, get help, and join our community!

When I run ‘make’, I get the following error.

```plaintext
g++ -DBIT_VERSION -O3 -DRELEASE_DATE="\"2/2/2017\"" -DVERSION="\"1.39.1\"" -DUSE_READLINE -DUSE_BOOST -I "\"/home/mpiuser/bin/boost_1_63_0/include\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -o source/averagelinkage.o source/averagelinkage.cpp
In file included from source/datastructures/sparsedistancematrix.h:12,
                 from source/cluster.hpp:4,
                 from source/averagelinkage.cpp:5:
source/mothur.h:21:52: error: boost/iostreams/filtering_stream.hpp: No such file or directory
source/mothur.h:22:47: error: boost/iostreams/filter/gzip.hpp: No such file or directory
source/mothur.h:73:33: error: readline/readline.h: No such file or directory
source/mothur.h:74:32: error: readline/history.h: No such file or directory
In file included from source/datastructures/sparsedistancematrix.h:13,
                 from source/cluster.hpp:4,
                 from source/averagelinkage.cpp:5:
source/mothurout.h:113: error: 'boost' has not been declared
source/mothurout.h:113: error: expected ',' or '...' before '&' token
source/mothurout.h:114: error: 'boost' has not been declared
source/mothurout.h:114: error: expected ',' or '...' before '&' token
source/mothurout.h:114: error: 'int MothurOut::openInputFileBinary(std::string, std::ifstream&, int)' cannot be overloaded
source/mothurout.h:113: error: with 'int MothurOut::openInputFileBinary(std::string, std::ifstream&, int)'
make: *** [source/averagelinkage.o] Error 1

```

What is going on???

So, per INSTALL.md I went head and moved the gzip and the zlib

```plaintext
$ find /home/mpiuser/bin -type f -name "gzip.cpp"
/home/mpiuser/bin/boost_1_63_0/libs/iostreams/src/gzip.cpp
$ cp /home/mpiuser/bin/boost_1_63_0/libs/iostreams/src/gzip.cpp /home/mpiuser/mothur-1.39.2/source/
$ cp /home/mpiuser/bin/boost_1_63_0/libs/iostreams/src/zlib.cpp /home/mpiuser/mothur-1.39.2/source/

```

Then ran ‘make’. Got the same error. How can I get a mother MPI build? What am I not understanding?

Thanks in advance!

---

<div class="post-metadata">

**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [February 20, 2017, 12:47pm UTC](https://forum.mothur.org/t/mothur-mpi-make-error/3133/2 "2017-02-20T12:47:13Z")

</div>

It looks like boost is getting installed in the wrong place. FWIW, we have yet to see any benefit using MPI, in fact, for most of our parallelization it actually runs slower at times than using the processors options.

---

<div class="post-metadata">

**Author:** ![heyheyhey](https://avatars.discourse-cdn.com/v4/letter/h/da6949/32.png) [@heyheyhey](https://forum.mothur.org/u/heyheyhey)\
**Post date:** [February 20, 2017, 8:54pm UTC](https://forum.mothur.org/t/mothur-mpi-make-error/3133/3 "2017-02-20T20:54:56Z")

</div>

That’s what I was figuring. I probably need root privileges to get it where it needs to go. Thanks for the quick response! and the MPI advice.

---

<div class="post-metadata">

**Author:** ![heyheyhey](https://avatars.discourse-cdn.com/v4/letter/h/da6949/32.png) [@heyheyhey](https://forum.mothur.org/u/heyheyhey)\
**Post date:** [February 21, 2017, 5:13pm UTC](https://forum.mothur.org/t/mothur-mpi-make-error/3133/4 "2017-02-21T17:13:14Z")

</div>

Figured it out! Wanted to give an update. Here’s what I did.  
Running CentOS  
Followed this manual —\> [https://www.mothur.org/wiki/Installation](https://www.mothur.org/wiki/Installation)

Logged in as root.

```nohighlight
$ cd /usr/local
$ wget http://sourceforge.net/projects/boost/files/boost/1.63.0/boost_1_63_0.tar.gz
$ tar -zxvf /home/mpiuser/bin/boost_1_51_0.tar.gz
$ cd boost_1_63_0
$ ./bootstrap.sh --prefix="/usr/local/boost_1_63_0/boost"
$ ./b2
$ wget https://github.com/mothur/mothur/archive/v1.35.1.zip
$ unzip v1.35.1.zip
$ cd mothur-1.35.1
$ vim ./source/makefile

```

USEMPI ?= yes  
64BIT\_VERSION ?= yes  
CXX = g++44 (uncommented)  
#TARGET\_ARCH += -arch x86\_64 (commented)

```nohighlight
$ cd ./source
$ make

```