I could can align first line with other lines

\dfrac{\partial^2 P_{ijl}}{\partial \tau_l \partial \phi} & = &\dfrac{\partial}{\partial \tau_l}\left(P_{ijl}(1-P_{ijl})\frac{\partial \eta_{ijl}}{\partial \phi}\right) \\

& = &\dfrac{\partial P_{ijl}}{\partial \tau_l}\left(1-P_{ijl}\right)\frac{\partial \eta_{ijl}}{\partial \phi}+\frac{\partial \left(1-P_{ijl}\right)}{\partial \tau_l}P_{ijl}\frac{\partial \eta_{ijl}}{\partial \phi}+P_{ijl}(1-P_{ijl})\frac{\partial }{\partial \tau_l}\left(\frac{\partial \eta_{ijl}}{\partial \phi}\right) \\

& = &  ${P_{ijl}}{(1-P_{ijl})^2}$\dfrac{\partial \eta_{ijl}}{\partial \phi}-P^2_{ijl}\left(1-P_{ijl}\right)\frac{\partial \eta_{ijl}}{\partial \phi}+0 \\

& = &  ${P_{ijl}}{(1-P_{ijl})}(1-{2P}_{ijl})$\dfrac{\partial \eta_{ijl}}{\partial \phi}
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    Welcome to TeX.SX! You can have a look at our starter guide to familiarize yourself further with our format. – jub0bs Jun 29 '14 at 13:13
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    Welcome to TeX.SX! Please complete your example in order to make it compilable for us. This should contain a documentclass and all packages you need for reproduction of your error. – LaRiFaRi Jun 29 '14 at 13:13
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    tex.stackexchange.com/q/196 ; do not use $ in your equation as you are already in math mode. Don't use blank lines in your eqnarray. – LaRiFaRi Jun 29 '14 at 13:19
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    Use align, not eqnarray. This may help: tex.stackexchange.com/questions/98397/enumerate-formulas/… – Ethan Bolker Jun 29 '14 at 13:20
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    Please provide a full minimal example such that we can copy and paste your example and test it for our self. We cannot see which class you are using or which packages. That stuff matters. – daleif Jun 29 '14 at 14:01
% arara: pdflatex


\md{P_{ijl}}{2}{\tau_l}{}{\phi}{} &=\pd{}{\tau_l}\bigg(P_{ijl}(1-P_{ijl})\pd{\eta_{ijl}}{\phi}\bigg) \\
&=\pd{P_{ijl}}{\tau_l}(1-P_{ijl})\pd{\eta_{ijl}}{\phi}+\pd{(1-P_{ijl})}{\tau_l}P_{ijl}\pd{\eta_{ijl}}{\phi}+P_{ijl}(1-P_{ijl})\pd{}{\tau_l}\bigg(\pd{\eta_{ijl}}{\phi}\bigg) \\
&=P_{ijl}(1-P_{ijl})^2\pd{\eta_{ijl}}{\phi}-P^2_{ijl}(1-P_{ijl})\pd{\eta_{ijl}}{\phi}+0 \\
&=  P_{ijl}(1-P_{ijl})(1-2P_{ijl})\pd{\eta_{ijl}}{\phi}

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    You find better definitions of the commands in commath here – egreg Jun 29 '14 at 14:08
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    You are welcome! Next time, please reduce your code until you get it compilable. Errors like blank lines, missing {} or useless $$ can be found easily. Have fun TeXing. – LaRiFaRi Jun 29 '14 at 14:21

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