Give the correct permissions to file "install" in order to be able to execute it:
$ chmod +x install

Make sure that the nvcc compiler is in your path:
$ echo $PATH
/usr/local/cuda/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/local/bin

If nvcc is not in your path, you can add it using the following commands:
$ PATH=$PATH:/usr/local/cuda/bin
$ export PATH

Finally, check if the nvcc compiler is now in your path:
$ which nvcc
/usr/local/cuda/bin/nvcc

Make sure that the CUDA libraries are in your $LD_LIBRARY_PATH environment variable.
$ echo $LD_LIBRARY_PATH
/usr/local/cuda/lib64:/usr/local/lib:/opt/local/lib:/opt/local/lib/intel

If CUDA libraries are not in your $LD_LIBRARY_PATH environment variable, you can add them using the following commands:
$ LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64
$ export LD_LIBRARY_PATH

Finally, check if the CUDA libraries are now in your $LD_LIBRARY_PATH environment variable:
$ echo $LD_LIBRARY_PATH
/usr/local/cuda/lib64:/usr/local/lib:/opt/local/lib:/opt/local/lib/intel

Assuming the installation files are placed on a folder named "blast", the tree structure of the folder "blast" should look like:

blast
|-- database
| |-- env_nr
|-- gpublast
| |-- ncbi_blast_files
| | -- .
| | -- .
| | -- .
| |-- gpu_blastp.c
| |-- .
| |-- .
| |-- .
|-- ncbi-blast-2.2.28+-src/
| |-- c++
| | |-- compilers
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- GCC482-ReleaseMT64
| | | |-- bin
| | | | |-- blastp
| | | | |-- makeblastdb
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- build
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- inc
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- lib
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- status
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | |-- include
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- scripts
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- src
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- config.log
| | |-- configure
| | |-- Makefile
|-- queries
| |-- SequenceLength_00000002.txt
| |-- .
| |-- .
| |-- .
| |-- SequenceLength_00004998.txt
|-- install
|-- README

Calling ./blastp -db ../../../../database/sorted_env_nr -query ../../../../queries/SequenceLength_00000100.txt -gpu t -method 2
that means that there is a folder "queries" inside "blast" directory that contains a file "SequenceLength_00000100.txt" that contains a query.
Make sure that this file exists.

If during execution you get the message:
WARNING: Not enough GPU global memory to process volume No. 00 of the database. Continuing without the GPU...
            Consider splitting the input database in volumes with smaller size by using the option "-max_file_size " (e.g. -max_file_sz 500MB).
            Consider using fewer GPU blocks and then fewer GPU thread when formatting the database with (e.g. "-gpu_blocks 256" and/or "-gpu_threads 32") to reduce the GPU global memory requirements.

then your GPU does not have enough global memory to carry out the sequence alignment of the current database volume under the current GPU database configuration. To overcome this problem, you can reformat the database with "makeblastdb" with a value for "-max_file_sz" smaller than your previous choice. Another option is to recreate the GPU database by using the options "-method 2" and smaller values for "-gpu_blocks" and/or "-gpu_threads" than your previous choices (or use smaller values than 512 and 64 if you let GPU-BLAST create the GPU database with the default values as shown in the example above).

This error could be generated for several reasons:
1. Verify that you have a CUDA-capable GPU
2. Verify that you have installed CUDA toolkit